||||
|\/|
|/\|
||||

SIB-PAIR 0.99.9 (27 May 2003)

by

David L. Duffy

(1995-2003)

A program for elementary genetical analyses

David L. Duffy, MBBS PhD.
Queensland Institute of Medical Research,
300 Herston Road,
Herston, Queensland 4029, Australia.
Email: davidD@qimr.edu.au

Introduction
Methods
Usage
Datasets
Tips and tricks
Documentation of routines
Limitations
References
Program history

INTRODUCTION

Program Sib-pair performs a number of simple analyses of family data that tend to be "nonparametric" or "robust" in nature. It is modelled to some extent on the Genetic Analysis System [Young, 1995] in terms of the command language and types of analysis. Included are routines for:

Imputation of genotypes where unequivocal.
Allele frequencies in codominant genetic systems.
Segregation ratios for a binary trait.
Familial correlations and sibship variances for a quantitative trait. Variance components analysis of quantitative traits.
Haseman-Elston sib-pair regression for a quantitative (or binary) trait using full and half-sib data, and variance components linkage analysis for normally distributed quantitative traits.
Fulker and Cardon interval Haseman-Elston regression for a quantitative (or binary) trait.
Multiple allele versions of the transmission-disequilibrium test.
Test allelic association with a binary or quantitative trait -- Monte Carlo simulation of null distribution.
Single locus Affected Pedigree Method identity-by-state and identity-by-descent linkage analysis. This includes Wards [1993] extensions to include unaffected pedigree members.
Writes locus and pedigree files in the formats used by the programs APM, Arlequin, ASPEX, CRIMAP, FISHER, GAS, GDA, Genehunter, LINKAGE, LOKI, MENDEL, MERLIN, PAP and SAGE.

An example of use

Sib-pair is command line oriented, and writes output only to the standard output (the screen if you are using it interactively). Therefore output can be saved to a file only in batch mode, or via another program that can copy from the standard output, such as tee.

Bearing this in mind, here is a sample interactive session. We start at the command line of your operating system shell:

> sib-pair

A double arrow command prompt appears. We read in a previously prepared script:

>> include ex.in

The contents of ex.in are a series of Sib-pair commands:

# declare four loci set loc a affection set loc b quantitative set loc m1 marker 0.0 cM set loc m2 marker 5.1 cM # read the pedigree data read ped inline ex1 1a x x m n x 1 3 1 2 ex1 1b x x f n x 1 2 3 4 ex1 2a 1a 1b m n 3.5 1 2 1 3 ex1 2b x x f n 1.1 2 2 2 3 ex1 3a 2a 2b m y 4.3 1 2 1 2 ex1 3b 2a 2b m n 2.0 2 2 2 3 ex1 3c 2a 2b f n 0.8 2 2 3 3 ex1 4a 3c 3d f y x 1 2 2 3 ex1 3d x x m n x x x x x ex1 4b 3b 3e m y 4.7 1 2 3 4 ex1 4c 3b 3f m n 1.6 2 2 1 3 ;;;; # The four semicolons ends the in-line data run

The "run" command actually starts the initial processing of the pedigree.

NOTE: Imputation level 1. Imputing untyped parental genotypes where unequivocal. Pedigree file = inline.ped Number of loci = 4 Locus Type Position ---------- ---- -------- a a 6 b q 7 m1 m 8-- 9 m2 m 10-- 11 Number of marker loci= 2 Bonferroni corr. 5% = 0.025321 Bonferroni corr. 1% = 0.005013 Bonferroni corr. 0.1%= 0.000500 NOTE: Creating dummy record for ex1-3e. NOTE: Creating dummy record for ex1-3f. NOTE: Father and mother of person ex1-4a appear to be swapped around. Reordering. NOTE: Person ex1-3e appears as a mother and sex was unspecified. Setting sex to female. NOTE: Person ex1-3f appears as a mother and sex was unspecified. Setting sex to female. Pedigree: ex1 No. members: 13 No. founders: 6 No. sibships: 5 Total number of pedigrees = 1 Number with only 1 member = 0 Total number of sibships = 5 Total number of subjects = 13 Total subjects genotyped = 10 ( 76.9%) Total number of genotypes = 20 Largest pedigree (members) = 13 (Pedigree ex1) Deepest pedigree (genrtns) = 4 (Pedigree ex1) Mean size of pedigrees = 13.0 Mean pedigree depth = 4.0 Mean size where >1 members = 13.0 Mean depth where >1 geners = 4.0 Number of imputed genotypes= 0 Number of pedigree errors = 0 Number of deleted records = 0

We obtain a few routine messages and summary statistics. The small table of Bonferroni corrections is a reminder that Sib-pair does not usually correct P-values for multiple tests; it is up to the user to decide what the appropriate significance thresholds are.

Blank records are created for named but missing parents. This is necessary, as a formal pedigree should have none or both parents present for each person.

>> ls a* b* m1 m2

The "ls" commands shows trait loci (with an asterisk appended), and marker loci.

>> drop $m >> ls >> undelete a* b* (m1) (m2)

The "drop" commands drops loci from the scope of subsequent commands, while the "undelete" command returns access to all loci.

>> describe m1
------------------------------------------------ Allele frequencies for locus "m1 " ------------------------------------------------ Allele Frequency Count Histogram 1 0.3000 6 ****** 2 0.6500 13 ************* 3 0.0500 1 * Number of alleles = 3 Heterozygosity (Hu) = 0.5105 Poly. Inf. Content = 0.4064 Number persons typed = 10 ( 76.9%)

The "describe" command gives summary information about loci. For marker loci, it tabulates simple allele counts and proportions in the dataset. For traits, it gives familial correlations or recurrence risks. The "tabulate" gives simpler tables:

>> tab a
a x: 2 y: 3 n: 8 >> tab a m1

------------------------------------------------ Cross-tabulation of "a " ... "m1 " ------------------------------------------------ m1 a 1/2 1/3 2/2 --------------------------------------- n 2 (.286) 1 (.143) 4 (.571) y 3 (1.00) 0 (.000) 0 (.000) No. complete observations = 10 LR contingency chi-square = 5.5 Degrees of freedom = 2 P-value =0.0643

There are a few other simple descriptive commands. The "count" command gives information about families and individuals:

>> count b>1 Count where "b > 1": < Pedigree Con=T Num ASPs Trios 4+ ---------- ----- ----- ----- ----- ----- ex1 6 13 1 0 0 Total 6 13 1 0 0

The "select" command selects pedigrees containing a specified number (or one or more) individuals meeting the criterion. The "print" command is individual oriented:

>> print b>1 Print where "b > 1": id=ex1-2b sex=f a=n b=1.1000 m1=2/2 m2=2/3 id=ex1-4c sex=m a=n b=1.6000 m1=2/2 m2=1/3 id=ex1-4b sex=m a=y b=4.7000 m1=1/2 m2=3/4 id=ex1-3a sex=m a=y b=4.3000 m1=1/2 m2=1/2 id=ex1-3b sex=m a=n b=2.0000 m1=2/2 m2=2/3 id=ex1-2a sex=m a=n b=3.5000 m1=1/2 m2=1/3 Number of matched persons = 6 out of 13 ( 46.2%) Number of matched pedigrees = 1 out of 1 (100.0%)

If we had instead issued:

>> keep $m >> print b>1

we would obtain:

Print where "b > 1": id=ex1-2b sex=f m1=2/2 m2=2/3 id=ex1-4c sex=m m1=2/2 m2=1/3 ...

The "associate" command gives results from family based tests of allelic association for a trait versus all active marker loci:

>> ass a -------------------------------------------------- Allelic association testing for trait "a " -------------------------------------------------- Marker Typed Allels Chi-square Asy P Emp P Iters ---------- ------ ------ ---------- ------ ------ ------ m1 10 3 1.9 0.3930 0.1575 127 AssX2-HWE . m1 1 3 1.1 0.5978 0.5978 23 RC-TDT . m2 10 4 0.9 0.8192 0.7692 26 AssX2-HWE . m2 1 4 2.1 0.4471 0.4471 160 RC-TDT .

The "sibpair" command gives results from regression based tests of linkage for a trait versus all active marker loci. The P-values for these tests can be "empirically" estimated by gene-dropping marker alleles under the null hypothesis of no linkage:

>> sib b simulate --------------------------------------------------------- Sham S+D H-E for trait "b " v. all markers --------------------------------------------------------- Marker FSibs HSibs t-value Asy P Emp P Iters ---------- ------ ------ ---------- ------ ------ ------ m1 3 1 2.6 0.1180 0.0288 695 H-E + m2 3 1 1.5 0.1908 0.2128 94 H-E .

Finally, we log transform the quantitative trait values and write out a Genehunter type pedigree file, so we can further examine our data using a multipoint program:

>> b=log(b+1) >> keep b -- m2 >> write locus gh b.loc dummy >> write gh b.pre dummy

The "dummy" keyword adds a dummy binary trait variable to the Genehunter pedigree file, so that program will calculate ibds for us. If we like, Genehunter can be run from within Sib-pair:

>> $ gh

The "$" command shells out to run another program. When we exit from Genehunter, we will be returned to Sib-pair:

>> quit This job took 1.8 minutes

There are a number of operations useful for manipulating pedigree data prior to analysis. These allow you to prune ("prune") pedigrees down to selected individuals and only those relatives needed to connect the index people, to reduce families to unrelated cases and controls ("case"), to break up large pedigrees into component nuclear families ("nuclear") or into unrelated cliques ("subped"), if the pedigree file does not specify all the connecting relatives (between different branches say). One can also select ("select" and "unselect") particular groups of pedigrees, and specify different values of a variable in each group:

# Select out ASP nuclear families >> nuclear >> select containing exactly 2 where dementia and isnon and anytyp # or EDAC nuclear families >> unselect >> select containing 1 where IgE>1000 and isnon and anytyp >> select containing 1 where IgE<50 and isnon and anytyp

Sib-pair also can be used as a calculator, and has a few genetics utilities, notably the "sml" and "grr" commands which gives expected recurrence risks, ibd's and genotype frequencies for a specified diallelic model:

>> sml 0.01 0.5 0.2 0.1 ------------------------------------------------ Single Major Locus Recurrence Risk Calculation ------------------------------------------------ Frequency(A): 0.010000; Pen(AA): 0.500; Pen(AB): 0.200; Pen(BB): 0.100 Trait Prev : 0.102020; Pop AR: 2.0%; Var(Add): 0.000206; Var(Dom): 0.000004 Measure MZ Twin Sib-Sib Par-Off Second ---------- ---------- ---------- --------- ---------- Rec risk 0.104 0.103 0.103 0.103 Rel risk 1.023 1.011 1.011 1.006 Odds rat 1.025 1.012 1.012 1.006 PRR 1.020 1.010 1.010 1.005 ibd|A-A 1.000 0.502 0.500 0.251 ibd|A-U 1.000 0.500 0.500 0.250 Freq of A if Affected: 0.019898 (0.000,0.039,0.961) Freq of A if Unaffctd: 0.008875 (0.000,0.018,0.982) Mating Proportion Risk to offspring ---------- ----------- ------------------ UnA x UnA 0.806 0.102 Aff x UnA 0.183 0.103 Aff x Aff 0.010 0.104

METHODS

Analytic Methods

Imputation of unobserved genotypes. This is performed using the algorithm described by Lange & Goradia [1987]. Firstly, (0) A phenoset (all possible genotypes) for one locus is generated for each individual in the pedigree. Then, iterate by nuclear families, repeating the next two steps until no further updates: (1) Parental genotypes inconsistent with their offspring are removed; (2) child genotypes inconsistent with their parents are removed. Finally, (3) If zero genotypes remain, report an inconsistency; if one genotype remains, this becomes the imputed genotype; if the joint spouse genotype is unambiguous, but the specific genotype each spouse carries is ambiguous, if requested, randomly assign a genotype to each parent. These latter genotypes are used only for calculation of statistics for offspring of the pair, but not for the parents themselves. A further extension is to sequentially (founders then nonfounders) impute the remaining missing genotypes as the most likely member of the phenoset. This is always performed to give starting values for the MCMC methods, but these simulated genotypes will not be saved unless the imputation level is set to "3" or "full".

Allele frequencies. These are for codominant systems only. Either a straight allele count is used, or the contribution of each pedigree is weighted by the number of founders it contains. Alternatively, the imputed and observed genotypes in the founders can be counted.

Hardy-Weinberg proportions. These are tested by a Pearson chi-square, with the P-value estimated via "gene-dropping" (Monte-Carlo,MC) simulation. These are based on the genotypes in the founders of that pedigree, where typed, or on the gene frequencies in the total sample where the founder is untyped, and the structure of the pedigree.

Segregation ratios. The default analysis assumes the pedigrees are unascertained, and gives the naive estimators. The ascertainment corrected analysis is for nuclear families and follows Davie [1979]: p=(r-j)/(t-j), where p is the risk, r is the total number of affected children, j, the number of sibships containing exactly one proband, t, the number of children. A fairly efficient approximate sampling variance is also given.

Haplotype reconstruction. This is performed on a nuclear family by family basis, though incorporating grandparental information where available. Initial reconstruction is performed using a simulated annealing algorithm that maximizes a sharing based criterion based on length of runs of the same alleles on a putative chromosome among sib pairs, parent-offspring pairs, and grandparent-child pairs. The order of loci in the pedigree file is treated as the linkage order, and map distance information is not used. Missing parental haplotypes are filled in using the childrens' haplotypes in a simple fashion. Mendelian inconsistencies are flagged in the printout.

The second algorithm is more ambitious and attempts to construct recombination minimized haplotypes, again on a nuclear family by family basis, and dealing more intelligently with missing data. A simulated annealing algorithm using multiple restarts is used. Recombination events and Mendelian errors are flagged in the output.

Admixture analysis. This refers to testing for a mixture of specified distributions in the empirical distribution of a quantitative trait, usually a mixture of normals, though Sib-pair also offers mixtures of exponential and Poisson distributions. Information from the relationship between family members is not utilised. The usual EM approach is used.

Test for normality. The Filliben correlation [Filliben 1975] is calculated as a test for normality. This is the correlation between the observed data and the rankits expected under the assumption of normality. The P-value for this statistic is approximate, and is produced using an approach modelled on that used by Royston [1993] for the related Shapiro-Francia W':

log(1-r_f) ~ N(m,s)
m:=1.0402 (log(log(n))-log(n)) - 1.99196
s:=0.788392/log(n)) + 0.31293

where n is the sample size. This performs reasonably well versus the empirical percentiles:

Coverage
n 5 10 20 50 100 500 1000 5000
Nominal P=0.05 0.021 0.044 0.055 0.057 0.059 0.052 0.045 0.033
Nominal P=0.01 0.00 0.006 0.009 0.014 0.019 0.007 0.007 0.007

	Coverage
n	5	10	20	50	100	500	1000	5000
Nominal P=0.05	0.021	0.044	0.055	0.057	0.059	0.052	0.045	0.033
Nominal P=0.01	0.00	0.006	0.009	0.014	0.019	0.007	0.007	0.007

A common use of the Filliben correlation is as the criterion for selecting an optimal transformation of the data.

The J_0.02 statistic is a variance-corrected order-statistic based skewness measure:

[(P_0.02+P_0.98)/2-P_0.50]/[P_0.75-P_0.25]

[David & Johnson 1956]. A test of normality can be constructed, using the standard error of J_0.02. This is based on interpolation of results from Monte-Carlo simulations (SE(J_0.02):=1.36/sqrt(N) cf Resek [1974]).

Sibship variance test. This is the linear model suggested by Fain [1977] for the detection of the phenotypic effects of quantitative trait loci. Briefly, if parental trait values are at the extreme of the population distribution, then they will be carrying multiple increasing or decreasing alleles at the QTLs. As a result, the trait variance among their offspring is decreased compared to sibships whose parents have trait values close to the population mean. This U-shaped relationship between midparent value and sibship variance can be detected by fitting linear or quadratic curves.

Variance components analysis. This is the usual analysis of quantitative traits assuming multivariate normality. The log-likelihood:

LL = -0.5 [log(det(S)) + (y-u)' inv(S) (y-u)]

is maximized, where S is the variance-covariance matrix for the trait values for each phenotyped pedigree member, and y and u are the trait values and their expected values (the overall trait mean). The main diagonal elements of S takes the value:

V_A+V_Q+V_D+V_E,

and the off-diagonal elements:

R_i,jV_A+ibd_i,jV_Q+K_i,jV_D,

where,

R_i,j is the coefficient of relationship for the i-jth pair of relatives
K is the coefficient of fraternity
ibd is the average ibd sharing at the marker location being tested for linkage to a QTL.

The maximization is performed using AS319 (variable metric minimizer with numerically estimated gradients). The phenometric models (ADE, AE, E) are fitted to the intact entire pedigree, but the models including V_Q are fitted to sibships only (at present).

Binary trait association analysis. This is the Pearson goodness-of-fit based test for equality of allelic gene frequencies at a marker locus in individuals expressing or not expressing a binary trait (2xN table). Both the nominal (ignoring relatedness of the sample) and empirical P-values for the test are output. The empiric P-value is estimated via gene-dropping simulation. These are based on the gene frequencies in the total sample, and the structure of the pedigree, and are conditional on the observed occurrence of the binary trait in the families.

Formerly, a sibship permutation based test was provided, calculating the same chi-square statistic for members of sibships that contain at least one affected and one unaffected typed individual, and generating a (within-sibship) permutation P-value. This is now replaced by a more powerful score test combining the within-sibship association and transmission-disequilibrium tests after Knapp [1999] and Laird et al [2000]. In this approach, the complete or partial genotype of untyped parents is reconstructed from the genotypes of the affected and unaffected children. The transmission of alleles from these reconstructed parents is conditioned on the genotypes of the children used in the reconstruction. The appropriate conditional distribution under the null hypothesis is approximated via Monte Carlo simulation and rejection sampling.

Population genetic F statistics (F_IS, F_IT and F_ST) are also calculated for each marker assuming affected and unaffected individuals come from separate related demes. These are estimated following the approach of Pons and Chaouche [1995], as described by Excoffier [2001].

Quantitative trait association analysis. This fits an additive (allelic means) model predicting an individual's trait value from his/her genotype at a marker locus. The residual sum-of-squares is compared to those obtained via a gene-dropping simulation of the pedigrees, giving an empiric P-value.

Two-locus linkage disequilibrium estimation. This algorithm finds informative founder matings, or informative matings where all the grandparents are untyped, and imputes the two-locus haplotypes transmitted to the offspring. The loci are assumed to be tightly linked, so that four parental haplotypes are counted, as opposed to the more usual two haplotypes from the child. Both D and D' measures are calculated.

Homozygosity analysis. This tests for an increase in observed homozygosity at a marker locus in individuals expressing a binary trait, comparing this to the predicted homozygosity based on the allele frequencies in the total sample. This may occur in the presence of allelic association with a recessive trait locus, and/or deletional loss of heterozygosity (the parents would be untyped for such an individual not to have been flagged as a Mendelian inconsistency of course). A one-tailed empiric P-value is estimated via "gene-dropping" simulation, based on the gene frequencies in the total sample, and the structure of the pedigree.

Transmission-disequilibrium test. The original formulation of the TDT is for a diallelic marker [Spielman et al 1993]. The TDT statistic calculated by the program is the Pearson goodness-of-fit based test of symmetry in the square table of transmitted versus nontransmitted alleles to each affected child [Haberman, 1979]. Empiric P-values are produced by randomization of the table. This global allelic form does not correct for the (usually small) correlation in parental genotypes induced by linkage disequilibrium (absent of course under the null hypothesis). Another allelic test provided is the marginal allelic test suggested by Spielman and Ewens [1996], which is probably slightly more powerful than the global symmetry test [Kaplan et al 1997].

The genotypic TDT P-value is estimated via gene-dropping based on the genotypes of typed ancestors of probands (where both parents of the proband and all antecedents must be typed), and the structure of the pedigree. The test statistic compares the observed number of each genotype transmitted with the number expected based on the parental genotypes. Pairs of cells whose total count is less than a given cutoff may be excluded from the analysis to increase power. The P-value for the TDT testing each allele versus all others in turn ("allele-by-allele") is the exact two-sided binomial probability (via the beta distribution). When the plevel is zero, only the best of the allele-by-allele test results are printed, and the P-value is Bonferroni corrected for the number of alleles at that marker.

Note that the default option is to use probands for the TDT only one parent is typed. For the diallelic marker case with unequal allele frequencies, using one parent families does lead to biased results. The unified transmission test available via the "assoc" command does not suffer from this problem (see above).

The Schaid and Sommer [1993] genotypic risk ratio tests for familial association under the assumption of Hardy-Weinberg equilibrium, or conditional on parental genotypes, is also offered. This uses log-linear modelling (implemented as iteratively reweighted least squares) of a biallelic locus with both parents genotyped. The attributable risk is also produced.

Sib-pair analysis. Identity by descent estimation is based on the sib pair and parental genotypes when available. In the case of untyped parents, the full-sib sharing is the sum of sharing for each possible set of parental genotypes weighted by their likelihood based on all children in the sibship. Half-sib sharing is estimated based only on known genotypes, whether observed or unequivocally imputed. The effective degrees of freedom for the t-test of the slope of the regression line is given as the number of individuals in the sample (counted once only) who are in a sib pair where both members are typed at trait and marker, minus two. For a sample made up of nuclear families (no halfsibs), this will be equivalent to the SUM(sibship size-1)-2 value used by SIBPAL 2.6, and originally suggested by Hodge [1984]. For binary traits, the same ordinary-least-squares analysis is performed -- the t-statistics from these results are only really applicable to large samples, and tend to be too liberal. The quantity regressed is not the usual Haseman-Elston squared trait difference, but a function of the squared trait sums and differences following Sham and Purcell [2001]. This approach is supposed to approach the power of the variance components approach according to those authors, and gives appropriate Type 1 error rates.

For the Fulker & Cardon methods, the expected ibd through the interval between the two markers is estimated using the equation given in Olson [1995]. Haseman-Elston regressions are performed at a series of points across the interval using the ibd sharing of the two flanking markers, and the given size of the interval. The Haldane mapping function is used.

Affected sib pair analysis. This is the original IBS based approach described by Lange [1986a], extended to half-sibs as per Bishop and Williamson [1990]. No correction for sibship size is made -- that is all possible pairs are treated as independent. The usual two d.f. chi-square is calculated, with expected counts being calculated based on the observed gene frequencies in the total sample. The IBD based mean test is also calculated.

Affected Pedigree Method. This uses the measures of genetic similarity described by Weeks and Lange [1988; see also, Lange, 1986a, 1986b], Whittemore and Halpern [1994], and Ward [1993, 1995]. The expected mean and variance for each pedigree is estimated via gene-dropping simulation. These are based on the observed gene frequencies in the total sample, and the structure of the pedigree. Both ibs and ibd based family scores can be estimated. The original APM statistics, the APM statistic of Whittemore and Halpern and the T(AB) and GPM statistics of Ward are calculated.

Multilocus IBS sharing statistics. These are used to confirm the pedigree structure using marker data. One approach calculates the overall probability of sharing two alleles IBS for full and half sibs, summing over all loci, and ignoring any linkage between markers. The second approach uses gene dropping based on the given marker map. Two lists are generated, one by individual, the other by relative pair.

Martingale residuals. The elegant approach of Commenges [1994] to genetic analysis of age-at-onset is to analyse the residuals obtained from a nonparametric or semiparametric survival analysis. Sib-pair implements the former, calculating the martingale residuals using the Nelson-Aalen estimator for the integrated hazard [eg Andersen et al 1993], which are then transformed following Therneau et al [1990] to give a more symmetrical distribution.

Monte Carlo Algorithms

Gene-dropping. The "unconditional" algorithm producing null distributions is as follows. Repeat the following 1-3 steps a large number of times. (1) Founder genotypes are assigned using the allele frequencies in the observed sample, assuming panmixia and Hardy- Weinberg equilibrium (HWE). Iterate, until all genotypes are assigned: (2) If both parental genotypes are nonmissing, randomly assign the index a genotype based on Mendelian autosomal inheritance (ie if parental genotypes are {1/2} and {3/4}, a child's genotype is randomly selected from {{1/3}, {1/4}, {2/3}, {2/4}}, with each genotype having a probability of selection of 0.25). Once complete, (3) calculate the test statistic based on the family's simulated genotype. Following completion of the outer loop, (4) summarize the distribution of the resulting test statistic. This procedure is used to generate null distributions for the association Pearson chi-square.

For the share command, this also allows for recombination between markers based on the given linkage map

The null distributions for the genotypic marginal TDT is generated using a "conditional on founders" algorithm, that takes observed founder/ancestor genotypes as given. Only typed nonfounders genotypes where both parents were typed are simulated.

ibd estimation. The modification to calculate ibd distributions gives each founder (two) unique alleles in his/her "typing genotype". A simple gene-drop gives the null distributions for the ibs and ibd statistics of the APM method.

I based the "conditional on observed genotypes" (gene-drop with rejection sampling) algorithm for calculating ibd on that described by Blangero et al [1995]. As before, each founder is assigned a typing genotype made up of two unique alleles. Offspring are only assigned ibd-typing genotypes that are consistent with the observed genotype at the observed locus of interest. For example, say the observed genotypes in the parents are 100/102 and 100/102, and the typing genotypes associated with these are set to {1/2} and {3/4} respectively. If the child is 100/102, assignment of typing genotypes {1/3} and {2/4} will be rejected. This is equivalent to a child's genotype being randomly selected from {{1/4}, {2/3}}, with each genotype having a probability of selection of 0.5. The resulting ibd statistics based on the typing genotype will approximate ibd for the marker locus of interest.

Missing genotype simulation by Monte-Carlo Markov Chain (MCMC). The calculation of ibd in the presence of missing genotypes is performed via a Metropolis algorithm. This algorithm is a multiallelic extension of that described by Lange and Matthysse [1989]. One iteration of the generation of a legal constellation of imputed and observed genotypes is produced by:

(1) Perform (a) (b) or (c):

(a) Simulate ibd, then "mutating" up to four imputed founder alleles. These propagate through the pedigree using the current pattern of ibd transmission as indicated by the ibd-typing alleles, and are rejected and resimulated if an (unordered) inconsistency with an observed genotype occurs.

(b) Simulate ibd, then switch the parent of origin for an individual heterozygote. Propagate this change up through the pedigree to the originating founder(s), but not below the chosen "pivot" individual.

(c) A "conditional on observed genotypes" dropping of ibd-typing alleles, with the refinement that this ignores imputed genotypes. Inconsistencies thus generated for imputed genotypes are resolved by changing the imputed genotypes. This procedure will be slow in the presence of a large number of untyped nonfounders.

(2) Resimulate all untyped x untyped founder mating joint genotypes conditional on their offspring and other spouses. This is included to speed mixing, and is not essential.

The resulting proposed constellation is accepted or rejected via the Metropolis criterion.

MCMC burn-in. In releases prior to version 0.96.0, there was no burn-in for this Metropolis algorithm, as preliminary empirical tests had found the results from this program agreed well with "exact" results from programs such as GENEHUNTER. Subsequently, I have found some pedigrees where using the starting genotypes from the Lange-Goradia approach does lead to biased ibd estimates for certain pairs of relatives. Therefore, the program now performs a number of burn-in iterations (default 100) prior to those used to estimate ibd. The required number of such iterations depends on the number of missing genotypes in the pedigree.

Randomized TDT. The randomization test for the global allelic TDT permutes the transmission table by randomly selecting a single proband-parent pair and reversing the transmitted and nontransitted alleles. One "shuffle" of the table involves N such permutations, where N is the number of such informative parent-proband pairs in the observed pedigrees (this reduces the correlation between successive tables in the random walk to close to zero).

Sequential empiric P-values. The Monte-Carlo P-values provided for the various MC-based tests are produced using the sequential approach described by Besag and Clifford [1991]. In this refinement, we only generate as many pseudosamples as is necessary to give a P-value numerator of size mincount; the denominator is the number of pseudosamples. The practical effect of this procedure is that if the true P-value is large, then relatively few pseudosamples are generated to give a less precise estimate of this uninteresting value. Besag and Clifford suggest a value for mincount of 10-20. It is necessary to set a maximum denominator to avoid excessive computation for "highly significant" results.

Other empiric P-values. An exception to this is the algorithm used for empirical P-values for the APM. Here, a P-value for each family is simulated at the same time as the mean and variance. These P-values were previously combined using the procedure due to Fisher [Hedges and Olkin 1985], that is, twice the sum of the natural logarithms of the P-values was treated as a chi-square variate with 2*N degrees of freedom, where N is the number of contributing families. This does not seem to be particularly powerful, so each P-value is now inverse-normal transformed to a Z-score, and these combined in an unweighted fashion [Hedges and Olkin 1985].

USAGE

The program reads commands from standard input, and writes results to standard output. Therefore, the program can be run interactively, or if a series of commands is to be found in a file, in batch mode. If the input file was test.in, entering "sib-pair <test.in >test.out" would perform the commands in test.in, and write results to test.out.

A command is a single line of keywords, locus names and/or variable values. If a "\" character is the last word of a line, the next line is interpreted as a continuation of the previous command. Sib-pair is case-sensitive, so that the keyword "READ" is not equivalent to "read". Commands are either global, which can be entered at any time; descriptive (set impute, set locus, read pedigree), which must precede the run statement; the run statement, that causes the dataset to be read and processed; or analytic, which act only after the run statement.

One command, set plevel, controls verbosity of output. Some useful descriptive tables are only printed if plevel is at least 1.

Sib-pair's parser can evaluate simple algebraic and logical expressions for each record in a datafile, but does not allow complex programming. For example, multiple actions contingent on a single condition usually have to each have their own if statement.

A peculiarity of the subsetting statements (keep, drop, undelete) is that they do not affect algebraic and logical expressions. Therefore, it is possible to drop a variable, but still use it to select pedigrees, say.

Global commands

!|#. The rest of the line is a comment, and is echoed to standard output.
%|$. The rest of the line (up to position 80) is a command, and is passed to the shell for execution.
clear. Restarts the program, closing all workfiles and zeroing all arrays.
help [all|globals|data|analysis]. Prints a brief description of the commands -- either all, or a subset.
info. Information about program settings.
list|ls [markers|$m|traits|$a|$q]. List of loci in current analysis.
show map. Shows the current marker map.
time. Print time elapsed since start of the program.
include <command file>. Read in Sib-pair commands from a file.
quit|bye. Halts the program.
set prompt [on|off]. Displays a prompt.
set ndecimal_points [<nwid>] <ndec>. The total width (number of characters) of a quantitative variable written to a new pedigree file defaults to 9 (and is fixed to 8 for some files, notably MENDEL and FISHER) but can be set as high as 20 for GAS and LINKAGE format files. The number of decimal places can be set to ndec.
set out|plevel <level>|verbose|on|off. Increasing the print level causes more information to be printed by almost all procedures. Print level 1 prints out the identities and genotypes of parents imputed where the genotype was missing, raw counts of genotypes for the hwe procedure, expected ibs probabilities for the asp procedure etc. Print level 2 (or verbose) writes out the statistics for each simulated dataset for the MC based procedures, the intrapair variance and ibd sharing for each pair in the sib pair analysis, etc. Print level -1 omits outputting a list of pedigrees.
set weight founders|imputed. Weights contribution of each pedigree to the allele frequencies by the number of typed founders, or alternatively gives the count of the founder alleles, observed and imputed.
set burn-in<number of iterations>. Controls the number of Markov Chain Monte-Carlo iterations used by the apm algorithm discarded before estimation commences. Default is 100 iterations. Setting bur to zero means no burn-in is performed (the old default).
set iteration<number of iterations>. Controls the number of iterations used by the various Monte Carlo algorithms. Default is 200 iterations. Setting ite to zero means the Monte Carlo procedures are not performed.
set mincount <minimum numerator of P-value>. Controls the number used for Monte Carlo simulation of a P-value. Default is 20 pseudosamples with a test statistic more extreme than that for the observed statistic. Set mincount equal to iter if this is not desired.
set seeds <seed1> <seed2>< seed3>. Initializes random number generator seeds to given values, rather than via system time.
set tdt bot[h parents]|one [parent]|first. Limits TDT statistic to cases where either both parents or at least one parent is typed, or one proband per family where both parents typed.
set map function kosambi|haldane. Set the mapping function used by multipoint analytic and locus file output routines.
pchisq <chi-square> <degrees of freedom>. Calculate P-value for central chi-square distribution.
proportion <numerator> <denominator> <confidence interval width>. Calculate accurate confidence interval following Wilson (as described by Agresti and Coull) for a proportion.
sml <Frequency of A allele> <Penetrance of AA genotype> <Penetrance of AB genotype> <Penetrance of BB genotype>. Calculates recurrence risks and segregation ratios under a specified diallelic generalized single major locus model.
sml <Frequency of A allele> <Mean for AA genotype> <Mean for AB genotype> <Mean for BB genotype> <standard deviation for AA genotype>. [<AB SD> [<BB SD>]]. Calculates mean, variance components and parent-offspring regression results under a specified diallelic generalized single major locus model.
grr <trait prevalence> <Frequency of A allele> <genotypic risk ratio> [add|dom|rec]. Calculates recurrence risks and segregation ratios under a diallelic generalized single major locus model specified via trait prevalence, ratio of penetrances and pattern of inheritance (codominant multiplicative, dominant or recessive).
Algebraic operators and functions
<value>|<locus> *|/|+|-|^ <variable>|<locus>. Arithmetic operations combining numerical constants and/or trait values. The result of an operation involving constants is a single constant, but an operation involving a trait value results in nobs results (where nobs is the number of individuals in the pedigree file.
<value>|<locus> <|>|ge|le| eq|==|ne|^=|and|or <variable>|<locus>. Logical operations comparing numerical constants and/or trait values.
if <logical expression> then <action> [else if <logical expression> then <action>]... [else <action>]. Conditional evaluation of expressions. Note that if statements cannot be nested.
log|sqrt|exp|sin|cos|tan|asin|acos|atan|abs|int|round <variable>|<locus>. Functions acting on numerical constants and/or trait values.
rand|rnorm. Produce a random value from U(0..1) or N(0,1).
istyp|untyp <marker>. Test if genotyped at given marker.
numtyp|anytyp|alltyp. Show number of markers an individual is genotyped at, or indicate whether genotyped at any one or all marker loci.
male|female|isfou|isnon. Test sex and founder status of individual.
num|nfound. Number of members and number of founders of the pedigree containing an individual.
famnum|index. Position of pedigree and of individual in the active dataset.
Data Declaration commands
set datadirectory <pathname>. Sets directory to be searched for pedigree files.
set workdirectory <pathname>. Sets directory to which temporary files are written.
set impute off|on|<level>. Toggles imputation routine.
- Imputation level 0 (off) does not impute genotypes. It does generate legal genotypes for all untyped individuals, that are used for the MCMC IBD estimation. This approach is slowed by, and can fail (stochastically) in large pedigrees. In this case, the imputation level can be set to -1 (completely off!).
- Imputation level 1 (on) imputes single individual's genotypes if unambiguous. All missing genotypes are silently imputed for the use of the MCMC IBD routine via sequential imputation and application of the Lange-Goradia algorithm (see level 3).
- Imputation level 2 imputes the genotypes of a spouse pair where the exact owner of each genotype is ambiguous eg both parents unknown, children 1/2, 3/4 so parental phenosets are each {{1/3},{2/4}}. Of limited use.
- Imputation level 3 makes available all the imputed values for the missing genotypes (in pedigrees where at least one member is typed at the locus). The missing genotype is replaced by the most likely genotype conditional on the typed members of the pedigree, and those genotypes imputed at that time -- single locus sequential imputation. Imputation proceeds through the untyped founders, according to the collation order of the ID, then nonfounders, according to the collation order of parental IDs.
set errordrop off|on|<level>. Toggles automatic deletion of genotypes that give rise to a Mendelian inconsistency, either an entire nuclear family (level 1), or an entire pedigree (level 2, the default).
set checking off|on. Toggles the first level testing for Mendelian inconsistencies within nuclear families.
set locus <locus name> <locus type>. Declares position (by order within list), name and type of locus within pedigree file. Locus type may be either:

marker an autosomal (fully) codominant marker
xmarker X-linked codominant marker
quantitative quantitative (or interval or ordinal) trait
affection binary trait

It is best to avoid a locus name containing reserved characters (eg "+-*/()^"), if algebraic manipulation of that variable will be required (othewise quotation of the name is required). Names identical to commands also cause trouble unless protected by brackets.
loci <command file>. Read in Sib-pair locus and pedigree file declarations from a file.
read locus linkage <locus file name. Read locus names, types and map positions from a Linkage-format locus (.dat) file. Does not recognise factor coding of genotypes.
read pedigree <pedigree file name>|inline. Reads a GAS type pedigree file either from an external file, or inline following the command. The inline data is terminated by a line containing ";;;;".
read linkage <pedigree file name>|inline. Reads a LINKAGE type pedigree file.
set sex on. Creates a quantitative dummy variable for sex (field 6 in pedigree file).
run. Reads in pedigree file and creates working pedigree file. Imputes genotypes if requested.
set map <pos1>...<posN>. Set map positions for the marker loci. This will overwrite any original map positions.
set distances <dis1_2> <dis2_3>...<posN-1_N>. Set interlocus map distances map positions for the marker loci. Distances are in centiMorgans. This will overwrite any original map positions.

Analysis and data manipulation commands

keep <loc1>...[<locB> to <locC>]... [$mar|$qua|$aff]...<locN>. Retain loci in subsequent analysis. Consecutive loci can be summarized as a range, as can all members of a particular class of locus type (marker, quantitative, affection) via a class ($type) token. Note that dropped variables can still be used in algebraic and logical expressions.
drop <loc1>...[<locB> to <locC>]... [$mar|$qua|$aff]...<locN>. Exclude loci from analysis. Note that dropped variables can still be used in algebraic and logical expressions
undelete [<loc1>...[<locB> to <locC>]... [$mar|$qua|$aff]...<locN>]. Return previously dropped loci to analysis. Default is to undelete all dropped loci. This is not the reverse of the delete command.
select [containing|exactly <nprobands>] [where] <a logical expression>. Select pedigrees containing one or more individuals with a trait value meeting the criterion.
select pedigree [[not] in] <ped1>...<pedN>. Select pedigrees included or excluded from a list of pedigree names.
unselect. Returns all pedigrees excluded by a select command back to the analysis.
pack. Permanently delete all pedigrees excluded by a select command from the work file.
edit <pedigree> <person>|all <trait> to <value> [<new value>]. Allows editing of trait values or genotypes. The all keyword performs the action on all members of that pedigree.
delete <pedigree> <person>|all Sets all data to missing for a specified individual. The all keyword performs the action on all members of that pedigree.
delete [<locus1>...<locusN>] [whe|where] <a logical expression>. Sets specified data to missing for all individuals meeting particular criteria.
recode <marker> <all1|value1>...<allN|valueN> to <new allele|new value>. Allows pooling of marker alleles prior to subsequent analysis.
combine <marker1> [...<markerN>] [<threshold>]. Pool rare alleles for a marker into one new allele. "Rare" defaults to a frequency of 5%, but can be changed via the last parameter on the command line.
transform <xtrait> <divisor> <subtractand> <power> <lower threshold> <higher threshold>. This transform the quantitative trait xtrait as:
boxcox({xtrait-subtractand}/divisor)
where boxcox() is (a slightly altered) Box-Cox transformation, so that:
- if power=0, the transformation is log({x-s}/d);
- if power=1, it is {x-s}/d;
- and otherwise [({x-s}/d)^p-1]/p.
The resulting transformed value can then be truncated above or below using a specified low or high threshold.
standardize <trait> [familywise]. Replace each trait value with its Z-score, ie (x-xbar)/sd, where xbar is the total sample mean, and sd the total sample standard deviation. This can also be performed using the individual's family mean and standard deviation, if the fam keyword is included.
adjust <ytrait> on <xtrait> [to <adjustment value of xtrait|m|f>]. Performs linear regression of quantitative trait ytrait on quantitative or binary trait xtrait (or sex, if sex is set to on), calculates residuals, and adds adjustment value or, if not specified, the mean value of xtrait. The residuals then replace the original values of ytrait. A multiple regressive adjustment of Y on X₁ and X₂ requires sequential adjustment of Y on X₂,X₁ on X₂, and then Y on the adjusted X₁.
residuals <ytrait> on <loc1>...[to]...<locN> [complete_obs]. Replace quantitative trait with the residuals from the multivariate regression on the list of predictors (which may include the average allele length of a marker locus). The com option means only individuals with no missing values for any of the listed traits will be updated. Otherwise, missing values are replaced with the sample mean for that phenotype when calculating the predicted value.
predict <ytrait> on <loc1>...[to]...<locN> [complete_obs] Replace quantitative trait with the predicted value from the multivariate regression on the list of predictors (which may include the average allele length of a marker locus). The com option means only individuals with no missing values for any of the listed traits will be updated. Otherwise, missing values are replaced with the sample mean for that phenotype. when calculating the predicted value
impute <ytrait> on <loc1>...[to]...<locN> [complete_obs] Replace missing quantitative trait values with the predicted value from the multivariate regression on the list of predictors (which may include the average allele length of a marker locus). The com option means only individuals with no missing values for any of the listed predictor traits will be updated. Otherwise, missing values are replaced with the sample mean for that phenotype when calculating the predicted value.
kaplan-meier <age-at-onset> <censor> [residuals]. Prints the product-limit estimator for the survivor function for the quantitative trait age-at-onset, where censor is the binary outcome trait, which is affected when age-at-onset represents the age at which the individual first expressed the trait. The age-at-onset is replaced by a nonparametric residual when requested. If affected, this is:
sgn(1-H(t)).(-2(1-H(t)+log(H(t))))^1/2
If unaffected:
-(-2H(t))^1/2
where H(t) is the Nelson-Aalen estimate of the integrated hazard function at that age t.
rank <trait> <rank>. Write the ranks of a quantitative trait to the quantitative variable rank.
nuclear [maxsibs] [grandparents]. Split pedigrees into component nuclear families, duplicating individuals as necessary. If maxsibs is set, then sibships containing more than maxsibs members are truncated. The gra option includes the grandparents as well.
subpedigrees. Split nominal pedigrees into component true pedigrees. Sib-pair normally can analyse a group of individuals with the same pedigree ID, even if they are not all related. This command splits such groups into uniquely named formal pedigrees.
prune [<binary trait> [|<quantitative trait> over|under <threshold>]]. Reduce pedigree to contain probands and minimum number of connecting relatives.
cases <locus>. Reduce pedigree to unrelated individuals with non-missing values at the trait i.e. the informative founders, and any informative nonfounders who are not directly related to any individuals already selected.
print [where] <a logical expression>. Print trait values for individuals, with a combination of trait values meeting the criterion.
write [<pedigree file name>]. Writes a GAS type pedigree file from the current dataset. Default is to screen.
write pap. Writes the required pedigree files trip.dat and phen.dat (note that you may have to sort trip.dat).

write	pedigree\|gas	<pedigree file name>
	arl		[par\|all]
	asp\|tcl
	crimap\|tcl
	dot
	fisher
	gda		[all]
	linkage\|gh		[dummy]
	mendel
	phe
	sage

Use of the keywords pedigree or gas writes a GAS type pedigree file from the current dataset. Quantitative values are written as F9.x or F8.4. The keyword gda writes a GDA Nexus datafile containing all current marker genotypes for founders. If the keyword all is added, nonfounders will be included as well, but the "gdatype" format will not differentiate between relatives. Similarly, arlequin writes a data file for the program Arlequin containing haplotypes from one informative child per family, or two parents of such a child if the par keyword is added. Only if the all keyword is added will all genotyped individuals be printed. The keyword linkage writes a pedigree file from the current dataset suitable for use by the LINKAGE (and FASTLINK) programs (note that if a quantitative trait value is zero -- that is nonmissing -- it is recoded to 0.0001); aspex (or tcl) writes a linkage style pedigree file but with the marker locus names as the first line, as the ASPEX programs prefer; gh writes a linkage style pedigree file with a dummy affection trait as the first trait and all the quantitative traits last, with "-" for missing quantitative trait values. The dummy option added to linkage or gh writes a dummy affection locus as the the first trait (everybody affected). The sage keyword writes a pedigree file from the current dataset suitable for use by the program FSP included in the SAGE package; mendel writes a pedigree file from the current dataset suitable for use by the programs MENDEL or SIMWALK; fisher writes a pedigree file from the current dataset suitable for use by the program FISHER; phe writes the "pheno.dat" style file required by Mapmaker-Sibs.

write map mendel|merlin|loki <map file name>. Writes out the map file required by MENDEL 4.0, MERLIN or LOKI.
write locus pap. Writes the required locus files header.dat and popln.dat.
write locus aspex|tcl <locus file name>
fisher
gas
linkage|gh [dummy]
loki
mendel
merlin
sage
sib-pair
Use of the keyword gas writes a GAS type locus file from the current dataset; linkage writes a locus file from the current dataset suitable for use by the LINKAGE (and FASTLINK) programs; gh writes the same as linkage save that map distances are in cM. The dummy option is used when the first trait is a dummy trait generated by write linkage <file> dummy. The keyword loki writes a control file for LOKI's prep program; sage writes a locus file from the current dataset suitable for use by the program FSP included in the SAGE package; mendel writes a locus file from the current dataset suitable for use by the programs MENDEL or SIMWALK; fisher writes a locus file from the current dataset suitable for use by the program FISHER; merlin for MERLIN; tcl or aspex writes the tcl command file required by ASPEX programs such as SIB_PHASE; sib-pair writes a Sib-pair style script.
generations [<quantitative trait>]. List founders/marry-ins and sibships by generation number for all pedigrees, (over)writing the generation number to a quantitative trait if requested.
haplotypes [<binary trait>]. This (still experimental) routine displays nuclear family (plus grandparental, where present) haplotypes as an ASCII pedigree drawing.
ancestors <binary trait> [|<quantitative trait> [over|under <threshold>]]. This prints the IDs of the ancestor (and ancestral mating) shared by the greatest possible number of probands in a family.
frequencies|describe [[<codominant marker>| <binary trait>| <quantitative trait>]...[to]...<trait>]. Print allele frequencies for marker loci, segregation ratios for binary trait, or means, variances, familial correlations and a sibship variance test for a quantitative trait. Default is to describe all loci.
count [where] <a logical expression>. Count individuals, and sibships and pedigrees containing such individuals, with a combination of trait values meeting the criterion.
print [where] <a logical expression>. Print phenotype data for individuals with a combination of trait values meeting the criterion.
tab <trait 1>...[<trait N>]. Print contingency table for one, two or N traits, along with contingency chi-square, Kruskal-Wallis test or odds ratio if appropriate.
kruskal-wallis <quantitative trait> <trait>. Print table of means for the quantitative trait for each level of factor, along with the Kruskal-Wallis chi-square.
regress <ytrait> on <x1>...[to]... <xN>. Performs linear or logistic regression of trait ytrait on set of loci x1...xN. If an x variable is a marker genotype, that independent variable is the mean allele size in the genotype.
mixture <quantitative trait> [<Number of distributions> [normal|pooled_normal|exponential|poisson]]. Estimate mixing proportions, means and standard deviations for a 1..5 component mixture model describing the specified quantititative trait. The default is a mixture of Normal (Gaussian) distributions with different means and variances, but a common variance can alternatively be specified. Other distributions available are the exponential and Poisson. A line-printer type histogram is produced.
kinship [inbreeding|pairwise]. Write the numerator relationship matrix (matrix of coefficients of relationship) for each pedigree in a lower triangular form or as a list of pairs (in the latter case, the coefficient of fraternity is also printed). Alternatively, if requested, print a list of individuals with a non-zero inbreeding coefficient.
ibd <codominant marker> [pairwise]. Write the estimated mean identity-by-descent sharing at a marker for all relative pairs in a pedigree as a lower triangular matrix or a list of pairs.
ibs <codominant marker> [pairwise]. Write the estimated mean identity-by-state sharing at a marker for all relative pairs in a pedigree as a lower triangular matrix or a list of pairs.
hwe [founders]. Prints chi-square statistic for Hardy-Weinberg equilibrium for all marker loci. Analysis may be restricted to founders. The mean IBS sharing for all typed matings is also calculated, and compared to its expected value. This latter test may allow detection of homogamy or assortment.
cksib. Lists all sib pairs, and the mean of IBS at all marker loci where both members of the pair are typed at the marker, comparing this to that expected if related as specified by the pedigree structure. The output is to the standard output.
share [pairs]. Lists all relative pairs, and the mean of IBS at all marker loci where both members of the pair are typed at the marker, comparing this to that expected if related as specified by the pedigree structure, allele frequencies and linkage map. The output is to the standard output. The default lists individuals whose Z score measuring deviation from expected exceeds 1.65 with any other relative. The pairs option prints the statistic for each deviant pair, or all pairs if output is set to verbose.
davie <binary trait> [<proband indicator>]. Print segregation ratios and standard errors for a binary trait, adjusted for the ascertainment scheme. Probands are indicated by being affected at the proband indicator "locus". If no proband indicator variable is given, complete ascertainment is assumed (equivalent to "davie trait trait").
varcomp <quantitative trait> [ae]. Performs MVN variance components analysis for a quantitative trait using all phenotyped individuals. Currently fits ADE, AE and E models. The ae option fits AE and E only.
dis [[<marker locus 1>] <marker locus 2>]. Estimates frequencies of two locus haplotypes based on individuals with two informative parents. The loci are assumed to be tightly linked, so that four parental haplotypes may be inferred. If no markers are specified, the sequence of pairs of markers in the list of loci is produced (ie marker1 with marker2, marker2 with marker3...). If one marker is specified, then the pairing of all other markers with this index marker is analysed.
assoc <binary trait> [|<quantitative trait> [over|under <threshold>]] [founders] [genotypic]. For a binary or dichotomised quantitative trait, prints chi-square statistics for association for all marker loci versus the trait, either affected versus unaffected if the trait is binary, or above or below the threshold if the trait is quantitative. A second table in the output shows the results from the reconstruction-combined TDT within informative sibships. Also prints F statistics assuming trait is marker for different subpopulations. For a quantitative trait, prints the model and residual sums-of-squares and allelic means with naive standard errors from an additive allelic ANOVA model. Monte-Carlo empiric P-values are produced for either analysis. Analysis may be restricted to founders. Genotypic rather than allelic analyses can also be specified, using the genotype flag.
homoz [<binary trait> [|<quantitative trait> over|under <threshold>]]. Prints the asymptotic Z statistic and a one-sided MC P-value for whether homozygosity at all marker loci is increased in probands, either affected if the trait is binary, or above or below the given threshold if the trait is quantitative.
tdt <binary trait> [|<quantitative trait> over|under <threshold>] [cutoff <cutoff>] [mat|pat]. Prints transmission-disequilibrium statistics for all marker loci versus the trait, where an index person is either affected with a binary trait, or whose value for a quantitative trait exceeds the given threshold. Since binary traits are coded internally as 2=y and 1=n, an analysis using unaffecteds as proband can be performed as tdt <binary trait> under 2. Similarly, in unascertained families, tdt <binary trait> over 0 tests for segregation distortion. Calculation of the TDT statistic can be restricted to pairs of cells whose total is greater than cutoff, eg 5, and to the maternal or paternal contributions, if parent-of-origin effects are suspected.
schaid <binary trait> <marker> [<allele>]. Performs the Schaid and Sommer [1993] genotypic risk ratio test for familial association under the assumption of Hardy-Weinberg equilibrium. Only one allele (defaulting to the commonest) is tested versus all others, and two penetrance ratios (GRR₂=f₂/f₀ and GRR₁=f₁/f₀) are estimated, along with the LR chi-square test that GRR₂=GRR₁=1.
asp <binary trait> [|<quantitative trait> over|under <threshold>]. Prints IBS-based affected (full and half) sib-pair statistics for all marker loci versus the trait. It also prints the mean IBD sharing for full sibs, along with the exact (binomial) two-tailed P-value for the "mean" test. All possible sib-pairs are used, and are treated as independent.
apm <binary trait> [|<quantitative trait> over|under <threshold>] [ibd|ibs]. Prints APM statistics for all marker loci versus the trait.
sibpair|he1|he2|vis <quantitative trait>| <binary trait> [<Weight variable>] [sim] [mean<trait mean>] [var | sd <trait variance or SD>] [cor<trait sibling correlation>]. Performs Haseman-Elston regressions (Sham & Purcell [2000] as the default, but Visscher-Hopper [Visscher & Hopper 2001], traditional and "new" Haseman-Elston also available) for all marker loci versus the trait using full and half-sib relative pairs. The contribution of each pair can be weighted by the mean of their values at a quantitative trait. Empirical P-values can be simulated, if requested. For the S+P regression, the "true" population trait mean, variance and sibling correlation can be specified, to facilitate analysis of selected samples.
twopair <quantitative trait>| <binary trait> <marker locus 1> <marker locus 2> <theta12>. Performs Fulker & Cardon's Haseman-Elston interval regression for first and second marker loci versus the trait using full- and half-sib relative pairs. The recombination distance between the markers theta12 must be given. Haseman-Elston regression is performed using ibd estimated at ten points in the interval.
qtlpair <quantitative trait>| Performs variance components linkage analysis for all marker loci versus the trait using full-sib relative pairs. Both the polygenic background and the QTL are modelled as additive genetic.
linkage [<marker locus 1> [<marker locus 2>]]. Performs Elston and Keats sib pair linkage analysis for codominant markers. Default is adjacent pairs of markers (ie marker 1 with marker 2, marker 2 with marker 3...). If one marker is named, then gives estimate of recombination distance to all other markers.

The following script performs a number of analyses on a dataset containing four loci.

Test.in

set work c:\tmp\
set weight founders
set out verbose
set impute on
set locus quant quantitative 
set locus trait affection 
set locus marker1 marker 
set locus marker2 nam
read pedigree test.ped
run 
freq
mix quant 2
assoc trait
tdt trait 
ass quant
sibpair quant
recode marker1 126 128 to 999 
freq marker1
tdt trait
apm trait
sibpair quant
! create a new trait
set locus new_quant qua
if (quant le 0) then new_quant= -sqrt(-2*quant) else new_quant=log(quant)
! adjust the binned allele sizes of marker
if (marker1 ne 999) then marker1=marker1+1
drop trait quant
write pedigree testout.ped

DATASETS

The data set contains one record (newline character delimited) per individual. Records must be sorted into pedigrees. Records take the format used by GAS:

pedigree-id person-id father-id mother-id sex-of-person locus-value-1...locus-value- N

A pedigree ID may be up to 10 alphanumeric characters, and an individual's personal ID up to 8 characters. Missing values are denoted x (or .), and represented internally as a trait value of -9999. Locus values for a binary trait are y (expresses trait), n (does not express trait). Sex takes the values m (male) and f (female), and may be missing. Alleles at a marker locus are integers between 1 and 999. A pedigree file may contain a comment at any time, prefaced by ! or #, and may contain a locus header of the form (though this has no function and is included to allow compatibility with the GAS pedigree format):

pedigree locus <locus-name-1>...<locus-name-N>.

If only one parent of an individual is specified in the pedigree file, a dummy record and ID number for the other parent is generated by the program.

Here is the data set analysed by the script test.in:

Test.ped

! test pedigrees including one halfsib in pedigree 1000
!                                          Marker 1  Marker 2
! The seven mating types:  1000-1 x 1000-2 Type VII  Type III
!                          1000-1 x 1000-3 Type VI   Type II
!                          1001-1 x 1001-2 Type IV   Type V
!                          
1000 1   x   x   m   10  y   126 132   1   1
1000 2   x   x   f   10  n   128 130   1   2
1000 3   x   x   f   25  n   128 132   2   2
1000 4   1   2   f   20  y   126 128   1   1
1000 5   1   2   m   30  y   130 132   1   1
1000 6   1   2   m   40  n   128 132   1   2
1000 7   1   2   f   50  n   126 130   1   2
1000 8   1   3   f   60  n   126 128   1   2
1000 9   1   3   m   40  y   132 132   1   2
1001 1   x   x   m   20  y   124 124   1   2
1001 2   x   x   f   30  n   126 128   1   2
1001 3   1   2   f   40  n   124 128   1   1
1001 4   1   2   m   30  n   124 126   1   2
1001 5   1   2   m   40  n   124 126   2   2
1001 6   1   2   m   40  n   124 128   1   2
1002 1   x   x   m   10  y     x   x   x   x
1002 2   x   x   f   40  n     x   x   x   x
1002 3   1   2   m   30  n   126 126   1   2
1002 4   1   2   m   60  n   126 126   1   1
1003 1   x   x   m   20  n   126 126   1   2
1003 2   x   x   f   25  n     x   x   x   x
1003 3   1   2   m   40  n   126 126   1   2
1003 4   1   2   m   15  y   126 126   1   2
! end-of-pedigrees

The pedigree file written by Sib-pair contains the original records plus any additional dummy records for missing parents of nonfounders. It is sorted by founder/nonfounder status, generation number, and the collation order of the parental IDs and individual ID.

TIPS AND TRICKS

How do I?

Get more output: Set the print level higher.
# # Get full TDT tables but summary results for association analysis # set ple 1 tdt trait set ple 0 ass trait
Analyse only selected traits: Use the drop then undelete commands to specify loci or ranges of loci to be included or exclude from particular analyses:
# Drop out year of birth and don't show any allele frequencies drop yob $m describe undelete
Write out only the markers: Use keep $m, then write pedigree. Note that this will undelete previously deleted markers.
Delete marker data for particular individuals: Use keep $m, then delete <pedigree> <person>, followed by und.
... set loc errprob qua keep $m delete where errprob>0.9 und
Use the new parser: This hopefully reduces the number of steps in data manipulation required for a complete analysis.
# # Create a new variable that is a function of # three existing quantitative variables # set loc b1 aff set loc q1 qua set loc q2 qua set loc q3 qua read ped ex.ped run set loc new_var qua new_var=log(q1+q2)/q3^2 if (male) then new_var=new_var+10 # # Select a subset of pedigrees where two or more probands # meeting multiple criteria # select containing 2 where new_var>35 and q1 le q2 and isnon write newped.ped
Use variable names in formulae when the variable name shares the first three letters with a command eg "trait" and "transform": surround the variable name with brackets.
Analyse multiple pedigree files: Jobs can be stacked, providing each begins with the clear command. The loci will have to be declared each time however.
Delete a marker that is giving too many mendelian inconsistencies: Use the drop command on that marker before the run command.
Ignore error messages from a marker that is giving too many mendelian inconsistencies: Drop the marker out before error checking as before, then use the undelete command before the hopefully robust type of analysis chosen. Alternatively set checking off and set impute -1 will turn off checking for all markers.
Test for segregation distortion: Do a TDT with everyone affected, for example, set sex on then tdt sex over -1.
Log transform a quantitative trait: Use tra trait 1 0 0 or trait=log(trait) (slower).
Get a histogram for a quantitative trait: Use the hist command (this is a synonym for mixture trait 1). Setting the print level higher for mixture also prints out posterior probabilities of membership of the different distributions -- useful for choosing thresholds.
Print genotype frequencies: Set plevel to 1 so that the full table is printed when the hwe command is used.
Remove unrelated individuals or nuclear families that have become disconnected from the main pedigree, although they have the same pedigree ID: Use the subped command, followed by select $n gt 20, or some other suitable number that will keep only the main pedigree.
Do a multipoint ASP linkage analysis: Write the appropriate format pedigree and locus file, and call another program like SIB_PHASE:
# Write a locus file write locus aspex batch.tcl # Write out the pedigrees as nuclear families (if multigenerational) nuclear write aspex batch.ped # The resulting output will be included in the Sib-pair output $ sib_phase -f batch.tcl batch.ped $ rm batch.tcl batch.ped

Which TDT result should I trust? The genotypic TDT is currently a more experimental test. In the case of nuclear families with typed parents, it reduces to a simulation based CPG GRR test. In larger pedigrees with multiple generations of affecteds, matings must have both parents genotyped before they are included in the simulation, but this is done over the complete pedigree.

What does the "founder" option for the allele frequencies give? Since a simple count of alleles in typed founders can miss alleles segregating in the pedigree (and thus inherited from untyped founders), I have provided a method that enumerates all alleles in each pedigree, but weights the contribution of the pedigree by the number of founders it carries (that is, the number of representatives from the population whose allele frequencies one is trying to estimate). So, in a simple example,

     1 1   x x               1 1   x x                
      |     |                 |     |
      +--+--+                 +--+--+            
         |                       |
   +-----+-----+                 |
  1 2   1 2   1 2               1 3

the contributions from each family would be weighed equally, as each contains two founders. For allele 1 for example,

Family 1      Family 2
  2 * 5/8  +  2 * 3/4       
 --------------------  =   11/16
   4 (total founders)

Allele 1 Allele 2 Allele 3
The naive estimate is: 8/12 (.67) 3/12 (.25) 1/12 (.08)
The weighted estimate: 11/16 (.69) 3/16 (.19) 2/16 (.13)
The imputation estimate: 6/8 (.75) 1/8 (.12) 1/8 (.13)
The MLEs (MENDEL USERM13): .6254 .2182 .1564

	Allele 1	Allele 2	Allele 3
The naive estimate is:	8/12 (.67)	3/12 (.25)	1/12 (.08)
The weighted estimate:	11/16 (.69)	3/16 (.19)	2/16 (.13)
The imputation estimate:	6/8 (.75)	1/8 (.12)	1/8 (.13)
The MLEs (MENDEL USERM13):	.6254	.2182	.1564

In this example, the frequencies of the 2 and 3 alleles are better estimated. In the imputation estimation approach, the untyped parents were imputed as 1/2 and 1/3 respectively.

What do I do if I have covariates or liability classes? Eventually the various binary trait analyses Sib-pair does will allow for covariates. At the moment, the best thing you can do is create multiple phenotypes eg male diabetes and female diabetes, with the phenotype set to missing appropriately. Then one can do the analysis within each stratum, and pool test statistics in various ways used in meta-analysis. In the case of quantitative traits, analysis of residuals formed by adjusting for covariates will carry you a long way.

DOCUMENTATION OF ROUTINES

Regression (multiple) is performed by AS (Applied Statistics) 164, which uses modified Givens rotations to perform weighted least squares regression including linear constraints. It is also used to give generalised linear models (poisson and binomial regression) via IRLS. The random number generator is the well known AS 183. The approximate randomization routine is styled after general templates described by Noreen [1989]. Mixtures of distributions are fitted using AS 203. Various standard distributions are evaluated using AS 3, 66, 111.

LIMITATIONS

Sib-pair currently is limited to a maximum of 600 (or 1000 or 2000) individuals per pedigree, 120 (or 1000) locus values or fields (eg 60 codominant genotypes, 120 binary traits etc), and 40 (or 60 or 100) possible alleles per codominant locus. The "low memory" version of the program stores phenoset for each individual in a pedigree is stored in a direct access file, with resulting overheads. Write to me if this sounds of use. The standard version performs imputation in memory. The Monte-Carlo based routines are computationally intensive. Generally speaking 200-300 iterations of such a routine are sufficient to give a good estimate of a mean or variance (as in the apm routine), but 1000 iterations or more are advised for an accurate P-value. Using "set iter 0" will provide only the parametric estimators, e.g. for screening purposes.

Sib-pair does not know about mitochondrial DNA.

There are only a few multipoint procedures (twopoint and haplotype).

The program is (fairly) standard Fortran 77, and runs successfully on PCs (under DOS, NT or Linux), SUN Sparcstations, DEC Alpha and HP9000 workstations. The current DOS version is compiled via f2c and the DJGPP port of the GNU C compiler, and is compressed using djp, an LZ0 executable compressor.

ACKNOWLEDGEMENTS

This program was developed while the author was an Australian National Health and Medical Research Council Neil Hamilton Fairley Postdoctoral Fellow and later a Research Fellow. This included a period working in the Genetic Epidemiology Division of the Johns Hopkins University School of Public Health and in the Epidemiology Unit at the Queensland Institute of Medical Research.

REFERENCES

Andersen PK, Borgan O, Gill RD, Keiding N (1993): Statistical models based on counting processes. New York: Springer Verlag.
Besag J, Clifford P (1991): Sequential Monte Carlo p-values. Biometrika 78: 301-304.
Bishop DT, Williamson JA (1990): The power of identity-by-state methods for linkage analysis. Am J Human Genet 46: 254-265.
Blangero J, Samollow PB, Rocha MB, Hixson JE, Rogers J (1995): The IGF1 locus is a major determinant of serum osteocalcin levels in Mexican Americans. Fourth Annual Meeting of the International Genetic Epidemiology Society, Snowbird, Utah, June 20- 22, 1995.
David F, Johnson NL (1956): Some tests of significance with ordered variables. J R Statist Soc B 18: 1-20.
Davie AM (1979): The 'singles' method for segregation analysis under incomplete ascertainment. Ann Hum Genet 42: 507-10.
Davis S, Schroeder M, Goldin LR, Weeks DE (1996): Nonparametric simulation-based statistics for detecting linkage in general pedigrees. Am J Hum Genet 58: 867-80.
Excoffier L (2001): Analysis of population subdivision. In: Balding DJ et al. Handbook of Statistical Genetics. London: Wiley and Sons. 271-307.
Fain PR (1977): Characteristics of simple sibship variance tests for the detection of major loci and application to height, weight and spatial performance. Am J Hum Genet 42: 109-20.
Filliben J (1975): The probability plot correlation coefficient test for normality. Technometrics 17: 111-117.
Haberman SJ (1979): Analysis of quantitative data. Volume 2. New developments. New York: Academic Press.
Haseman JK, Elston RC (1972): The investigation of linkage between a quantitative trait and a marker locus. Behav Genet 2: 3-19.
Hedges LV, Olkin I (1985): Statistical methods for meta- analysis. San Diego: Academic Press.
Kaplan NL, Martin ER, Weir BS (1997): Power studies for the transmission/disequilibrium tests with multiple alleles. Am J Human Genet 60: 691-702.
Keats BJ, Elston RC (1986): Determination of the order of loci on the short arm of chromosome 11 using two and three locus linkage analyses of pedigree and sib pair data. Genet Epidemiol Suppl 1:147-52.
Knapp M, Wassmer G, Baur MP (1995): The relative efficiency of the Hardy-Weinberg Equilibrium-likelihood and the Conditional on Parental Genotype-likelihood methods for candidate-gene association studies. Am J Hum Genet 57: 1476-1485.
Knapp M (1999): The transmission/disequilibrium test and parental-genotype reconstruction: the reconstruction-combined transmission/disequilibrium test. Am J Hum Genet 64: 861-870.
Kruglyak L, Daly MJ, Reeve-Daly MP, and Lander ES (1996): Parametric and nonparametric linkage analysis: a unified multipoint approach. Am J Hum Genet 58: 1347-1363.
Laird N, Horvath S, and Xu X (2000): Implementing a unified approach to family based tests of association. Genetic Epi 19(Suppl 1): S36-S42.
Lange K (1986a): The affected sib-pair method using identity by state relations. Am J Hum Genet 39: 148-150.
Lange K (1986b): A test statistic for the affected-sib-set method. Ann Hum Genet 50: 283-290.
Lange K, Goradia T (1987): An algorithm for automatic genotype elimination. Am J Hum Genet 40: 250-256.
Lange K, Matthysse S (1989): Simulation of pedigree genotypes by random walks. Am J Hum Genet 45: 959-970.
Lange K (1997): Mathematical and statistical methods for genetic analysis. New York: Springer-Verlag.
Noreen EW (1989): Computer-intensive methods for testing hypotheses: an introduction. New York: Wiley.
Olson J (1995): Robust multipoint linkage analysis. An extension of the Haseman-Elston approach. Genet Epidemiol 12: 177-194.
Olson J, Rao S, Jacobs K, Elston RC (1998): Linkage of chromosome 1 markers to alcoholism-related phenotypes by sib-pair linkage analysis of principal components. Genetic Analysis Workshop 11. September 8-10, Arcachon, France.
Pons O, Chaouche K (1995): Estimation, variance and optimal sampling of gene diversity. II. Diploid locus. Theor Appl Genetics 90: 122-130.
Resek RW (1974): Alternative tests of skewness: Efficiency comparisons under realistic alternative hypothesis. Proc Bus Econ Statist Section Am Statist Assoc 1974: 546-551.
Royston P (1993): A pocket-calculator algorithm for the Shapiro-Francia test for non-normality: An application to medicine. Statist Med 12: 181-184.
Schaid DJ, Sommer SS (1993): Genotype relative risks: methods for design and analysis of candidate-gene association studies. Am J Hum Genet 53: 1114-1126.
Sham PC, Purcell S (2001): Equivalence between Haseman-Elston and Variance-Components Linkage Analyses for Sib Pairs. Am J Hum Genet 68:1527-1532.
Spielman RS, McGinnis RE, Ewens WJ (1993): Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus. Am J Hum Genet 52: 506-516.
Spielman RS, Ewens WJ (1996): The TDT and other family-based tests for linkage disequilibrium and association [editorial]. Am J Hum Genet 59: 983-989.
Therneau TM, Grambsch PM, Fleming TR (1990): Martingale-based residuals for survival models. Biometrika 77: 147-160.
Visscher PM, Hopper JL (2001): Power of regression and maximum likelihood methods to map QTL from sib-pair and DZ twin data. Ann Human Genet 65: 583-601.
Weeks DE, Lange K (1988): The affected-pedigree-member method of linkage analysis. Am J Hum Genet 42: 315-326.
Ward PJ (1993): Some developments on the affected-pedigree-member method of linkage analysis. Am J Hum Genet 52: 1200-1215.
Ward PJ, Bonaiti-Pellie C (1995): Measuring gene-disease association using a general pair method. Genet Epidemiol 12: 681-686.
Whittemore AS, Halpern J (1994a): Probability of identity by descent: computation and applications. Biometrics 50: 113-117.
Whittemore AS, Halpern J (1994b): A class of tests for linkage using affected pedigree members. Biometrics 50: 118-127.
Young A (1995): Genetic Analysis System, version 2.0 [Computer program]. Oxford: Oxford University.

PROGRAM HISTORY

26-May-2003 (0.99.9)

Fixed infinite loop occasioned by last pedigree in file containing a pedigree error.

24-April-2003 (0.99.9)

The "del" command now accepts a logical expression defining those individuals whose data are to be deleted. The loci to be deleted can be given as a list. The "famnum" and "index" variables now contain the position of the family and that individual in the dataset.

17-April-2003 (0.99.9)

Prevented calculation of LD between X and autosomal markers.

10-April-2003 (0.99.9)

The "reg" command applied to a binary trait really does give the logistic regession. The "combine" command combines rare alleles at a marker into a single new allele.

09-April-2003 (0.99.9)

The "reg" command applied to a binary trait gives the logistic regression.

28-March-2003 (0.99.9)

Added "read locus linkage" to read locus information from a Linkage style .dat file.

20-March-2003 (0.99.9)

Recognise "/" as separating alleles in a pedigree file.

28-February-2003 (0.99.9)

Write "mainparams" and data file for Jonathan Pritchard's structure program ("wri str <datfil>", "wri loc str <locfil> <datfil>"). X chromosome TDT and allele frequencies, export locus files.

12-February-2003 (0.99.9)

Fixed bug in ordering of loci for "wri lin" (caused by introduction of X-linked marker class).

31-January-2003 (0.99.9)

Various changes to allow Mendelian error checking for X-linked markers. Defined "xmarker" as a class of variable.

23-January-2003 (0.99.9)

Fixed "tab", "dav", and "des" (for binary traits) so that they respect the new method of selection. Pedigrees are now marked as active or inactive, but not deleted -- need to "pack" (or write) for that. Quantitative variable printing in "pri" repaired.

22-January-2003 (0.99.9)

Fixed "edit" command fallout from addition of X-linked markers. Added "cas" command to divide pedigrees into unrelated cases and controls eg founders with information, or one child of parents with no information etc. The command "var <trait> ae" fits only the AE (and E) models.

17-January-2003 (0.99.9)

Genotypic association analysis option: "ass <trait> gen" gets a table of genotype rather than allele counts. The "unselect" command returns all pedigrees previously excluded by one or more "select" commands back into the analysis. A new type of marker "xmarker" added. Still sorting out the Mendelian error checking for this.

04-October-2002 (0.99.9)

Minimum intermarker map distance for Genehunter locus files fixed -- set to 0.01 cM.

18-October-2002 (0.99.9)

One too many recombination distances being written to LINKAGE locus files when a dummy locus specified. Thanks to David Evans for pointing that out.

17-October-2002 (0.99.9)

Improved nuclear family mendelian checker (back to former level!). Documented the "edit", "set errordrop", "set checking" and "delete" commands (as well as "prop" and "pchisq"). These shortcomings pointed out by David Evans. Added� "wri map merlin" command. A "xlinked" flag added to the "write locus linkage" command.

4-October-2002 (0.99.9)

If "set err_drop 2", then long-distance errors cause the entire pedigree to be set to missing for that marker.

25-September-2002 (0.99.9)

After the "nuc gra" command, a parent with missing parents could come after a nonfounder parent in the work file, causing a segfault on subsequent analysis.

18-September-2002 (0.99.9)

The "select pedigree" command allows inclusion or exclusion of specific named pedigrees from further analysis. The "gener" command now only lists summary information at the default print level. The "write pap" was writing MCMC start marker genotypes to the PAP phen.dat as if they were observed genotypes -- Sandra Hasstedt helped sort this out. Added a "write map" command, currently only for MENDEL map files. Changed default tdt to "both" -- both parents must be present.

29-July-2002 (0.99.9)

The "prune" command reduces a pedigree to the probands and a minimum number of connecting relatives. The "ancestor" with increased print level gives number of affected descendants for all individuals. Some code reorganisation.

01-July-2002 (0.99.9)

The "rank" command writes the ranks for a variable.

26-June-2002 (0.99.9)

Results of "and" and "or" operations with missing values are now more consistent (eg F && x = F). Bug in "dis <marker>" form of call to "dis" fixed (alleles at that marker were scrambled by the exact test). A "factor <marker> <trait>;" command allows genotypes to be coded as an quantitative variable (value 1...Ngenotypes).

20-June-2002 (0.99.9)

Can force calculation of Kruskal-Wallis test for RxC table using "kru <quantitative trait> <factor>".

19-June-2002 (0.99.9)

Can now print out values for selected pedigree members tested for by a conditional expression. The "tab" command extended to tables of arbitrary dimension.

12-June-2002 (0.99.9)

MCMC based "exact" test for LD added. Visscher and Hopper test repaired -- the squared trait sums were not centred (obviously, only affected unstandardised data). Peter Visscher pointed out and helped fix this.

28-May-2002 (0.99.9)

Added "numtyp", "alltyp" and "anytyp" automatic variables that report how many markers an individual is typed at. Cleaned up syntax for "des", "reg" to allow ranges of loci.

17-May-2002 (0.99.9)

Added Visscher & Hopper's version of Haseman-Elston ("vis"). The "gener" command can now write the generation number to a quantitative variable. Check and repair troublesome locus names, eg duplicates or reserved words.

17-Apr-2002 (0.99.9)

If "0" was used as a missing value for a binary trait, this was recognised as such: except for algebra. Now automatically recoded when read in. Thanks to Jacki Wicks for pointing this out. The "read linkage" command did not have this problem.

05-Apr-2002 (0.99.9)

Locus names as heading when write pedigree to screen. Documented and improved symmetry (skewness) test.

13-Mar-2002 (0.99.9)

A divide-by-zero error and internal read error (on some compilers) fixed. Thanks to Alexa Sorant for those reports.

12-Mar-2002 (0.99.9)

One last parser problem evaluating conditional expressions where the switch statement contains a missing value. When a variable is missing and is part of an expression other than equal or not equal ("==" and "^="), the expression evaluates to missing. The "if" statement was incorrectly carrying out the "then" branch rather than returning an error.

06-Mar-2002 (0.99.9)

Added F statistics to "assoc" command (assumes the binary trait indicates membership of a subpopulation). Cleaned up output of "assoc " command when no eligible individuals genotyped.

19-Feb-2002 (0.99.9)

Fixed bug is "istyp" and "untyp" command: these did not evaluate correctly when starting values for the genotypes were not imputed (ie "set imp -1" was used).

18-Feb-2002 (0.99.9)

Stopped segfault in RC-TDT when trait missing for any siblings. Genotypic TDT simulation not done for completely missing data.

15-Feb-2002 (0.99.9)

GH and linkage locus file map distances now written to 2 and 4 decimal places respectively.

31-Jan-2002 (0.99.9)

Sham and Purcell Haseman-Elston now has slope scaled and intercept fixed so that slope is estimated QTL genetic variance (as proportion of total). Also added keywords to "sib" to allow specification of the population trait mean, variance and sib correlation, so that selected samples can be analysed. Thanks to Anastasia Iliadou for prompting these changes.

23-Jan-2002 (0.99.9)

Write out control file for Loki's prep (pedigree preparation) program.

18-Jan-2002 (0.99.9)

Allowed estimation of dominance variance component in "var" command. Added QTLs to "sml" command.

11-Jan-2002 (0.99.9)

Added variance components analysis including QTL linkage analysis for full sibs.

3-Jan-2002 (0.99.9)

Fixed bug for RC-TDT under Windows , thanks to Lyle Palmer (program attempted to print contents of an unassigned variable).

29-Nov-2001 (0.99.9)

Added MC P-value for global RC-TDT.

27-Nov-2001 (0.99.9)

Fixed parent-of-origin TDT where parents and child all same genotype -- thanks to Emiko Noguchi for pointing this out. RC-TDT "allowed" to work when no unaffected children in dataset.

26-Nov-2001 (0.99.9)

Implemented the Reconstructed parents-Combined Transmission Disequilibrium Test (RC-TDT) of Knapp [1999], available through the assoc command, where it replaces the old sibship permutation test. This is essentially identical to the default test for binary data provided by the FBAT program of Xu, Horvath and Laird [2001].

16-Nov-2001 (0.99.9)

Uninformative sibships (all children same genotype) now stopped from diluting the sibship permutation test. Calculated genotypes are ordered by allele size.

15-Nov-2001 (0.99.9)

Reallow mother to precede father in list of parents of an individual. Pedigree errors now cause that family to be deleted (and an error message generated), rather than halting the program. Users should check a new line of the summary output eg:

Number of pedigree errors  =     1
Number of deleted records  =     4

02-Nov-2001 (0.99.9)

Several versions of how to handle missing data in expressions, especially where these recode data. At present, can test equality or inequality of a variable with missing (test missingness), but other operations evaluate to missing. Therefore, the expression "not male" is true when sex is missing, but "sex<2" is missing. Arithmetic expressions resulting in -9999.0 (the internal missing value code) now give -9999.0001.

11-Sep-2001 (0.99.9)

Fixed bug in evaluation of "<=", ">=" "==" "^=": precedence in complex expressions was not always correct. Added CPG chi-square to schaid output and loglinear modelling to the service subroutines (uses IRLS). Zeroing of genotypes when error dropping on changed so always deletes all genotypes for that nuclear family rather than attempting to guess where the error is (deleting child that gave rise to inconsistency).

04-Sep-2001 (0.99.9)

Fixed minor bug in qtdt() when zero subjects in a group: zero-trapped log routine use extended.

21-Aug-2001 (0.99.9)

Added "<=", ">=" "==" "^=" as synonyms for the logical comparisons.

17-Aug-2001 (0.99.9)

Better headings for "sib" output when plevel equal to 1. Matching on locus names now explicitly only on first 10 letters (an annoying feature was that declaring a locus name longer than 10 characters led to the name being truncated, but a "keep" command would use the full string). Result from "tab" fixed for case where only one level of a binary trait is present (eg affected only). Results of logical equality or inequality with missing now give true or false rather than missing.

14-Aug-2001 (0.99.9)

Added "count" and "linkage" commands. The latter follows Elston and Keats' approach (as seen in Sibpal!) to sib pair linkage of codominant markers, and is interesting (and likely to be replaced with something else). Fixed bug affecting "ne" keyword (code implementing had been deleted somehow!).

18-Jul-2001 (0.99.9)

Fixed bug in code implementing new Sham and Purcell Haseman-Elston.

17-Jul-2001 (0.99.9)

Made "else if" work. NB: you may not nest if statements, as in:
if b eq 1 then (if c eq 1 then d=1 else d=2) else d=3

The legal equivalent is:
if (b eq 1 and c eq 1) then d=1 else if (b eq 1 and c ne 1) then d=2 else d=3
or
if b ne 1 then d=3 else if c eq 1 then d=1 else d=2.

14-Jul-2001 (0.99.9)

Quoting blanks in some algebraic expressions no longer crashes the program eg "+" "".

10-Jul-2001 (0.99.9)

Nicer output from "tab", including results for a single variable and correct printing of genotypes.

6-Jul-2001 (0.99.9)

Added extra front ends to regress() so can access predicted values (for imputation) and multiple regression residuals: "predict" "residuals" and "impute". Fixed segfault occurring when "nuclear" met families of size 1.

5-Jul-2001 (0.99.9)

The output from "mix" now includes the Filliben correlation as a test for normality. The command "his" is a synonym for "mix 1".

28-Jun-2001 (0.99.9)

Adds "untyp()" and "round()" functions. Expressions involving genotypes evaluated for both alleles where appropriate, for example:
# If genotype missing, replace with new genotype allowing for different
# binning
if untyp D1S124 then D1S124=D1S124_2-1

20-Jun-2001 (0.99.9)

Fixed bug in famcor() where families of size 1 contributed to the count of matings. Quoting refined -- a quotation mark starts a new word, regardless of location. Added attributable risk to schaid procedure.

20-Jun-2001 (0.99.9)

Implemented improved combined Haseman-Elston regression of Sham & Purcell [2001]. Added quoting so special characters can be part of a variable name in mathematical and logical expressions.

19-Jun-2001 (0.99.9)

Rejinked selection criteria for TDT probands (1/2 x 1/2 -> 1/2 trios now contribute again) so that genotypic TDT mimics CPG GRR test (same expectations, uses unconditional chi-square as test statistic, but simulation reproduces conditional likelihood). Reintroduced "set wei imp" which counts the imputed and observed founder genotypes -- this is less accurate in small datasets (eg made up of nuclear families) than the unweighted or weighted versions.

18-Jun-2001 (0.99.9)

Fixed minor bug in writing MENDEL files: if zero had been used as a missing value for a binary trait locus in the original pedigree file, but the "read linkage" command not used, then this would be replaced by the last locus for the previous person when writing the MENDEL pedigree file. Added the Schaid and Sommer genotypic risk ratio test (HWE but not CPG, as latter overlaps the TDT).

14-Jun-2001 (0.99.9)

Fixed minor bug parsing negative arguments to commands (eg "set ple -1" was read as "set ple - 1"). Precedence of exponentiation lowered so "int(4.2)^2" gives 16 and not 17! And the size of evaluable expressions increased.

8-Jun-2001 (0.99.9)

Adds "inht" (inverse hyperbolic tan a.k.a. Fisher-Z transformation).

6-Jun-2001 (0.99.9)

The operator "<" was acting as ">" - corrected. Distributed DOS, Windows32/NT and Linux binaries are now compressed using UPX.

24-May-2001 (0.99.9)

Added more functionality to parser so allows (one level of) if-then-else construct, and creation and calculation of new variables. This extended to the "select" statement to allow arbitrary selection criteria to be specified. The "write" command with no arguments now writes to the screen. Quantitative variables can now be written up to 20 columns wide.

26-Apr-2001 (0.99.9)

If plevel is set to -1, Mendelian errors cause a list of possibly involved genotypes to be printed, rather than a pedigree drawing.

12-Mar-2001 (0.99.9)

Added "write dot" to produce drawing files for the dot graph drawing package (this does nice marriage node pedigree drawings). The "davie" command now adds the overall sibling recurrence risk. Default output from "apm", "asp", "ass", "hwe", "sib" and "tdt" is now a summary table with one line of output per test. The output print level must be increased by one to get the old output (slightly rearranged). Genehunter type pedigree files can be produced by "wri gh file [dummy]".

03-Oct-2000 (0.99.9)

The option "write arl file par" writes haplotypes from two genotyped parents per pedigree for Arlequin.

26-Sep-2000 (0.99.9)

Added "write arl" to produce haplotype files for Arlequin. Haplotypes from one child with genotyped parents per pedigree are output. The "hwe" table now includes genotype frequencies as well as counts.

20-Sep-2000 (0.99.9)

For PAP, families containing one member are now correctly recorded in trip.dat (as a parent of a dummy child, along with a a dummy spouse). The "grr" command calculates recurrence risks for a single major locus model parameterized in terms of prevalence and penetrance ratios.

26-Jul-2000 (0.99.9)

Fixed stupid error in "sib" command where half-sibs with one missing trait value were sometimes included in the analysis with trait value "-9999". Did not affect full-sib H-E regression. The "ibs" command writes out mean IBS sharing for all pairs, as "ibd" writes mean IBDs.

14-Jul-2000 (0.99.9)

Cleaned up bug in writing popln.dat, which expects only 5 allele frequencies per line. Now prints coefficient of fraternity when "kin pairwise" is used. Command "dis" estimates two-locus haplotype frequencies using independent or nearly independent informative matings.

23-Jun-2000 (0.99.9)

Fixed the obligatory equivalence problem, this time affecting "xta". Changed name to "tab". Added "sib-pair" as a locus file type.

15-Jun-2000 (0.99.9)

Added "all" as possible person ID for "edit" and "delete" command, allowing entire pedigree to be zeroed at a particular marker or phenotype.

13-Jun-2000 (0.99.9)

Corrected the P-values for the "he1 " command. This was giving the lower tail probability, rather than the upper tail probability.

08-Jun-2000 (0.99.9)

Pedigree and locus files produced for Genehunter 2 now have the loci automatically sorted. Added "xta" for RxC contingency tables for traits.

28-Feb-2000 (0.99.9)

Fixed stupid error introduced when fixing last one: caused segmentation fault in qtdt().

25-Feb-2000 (0.99.9)

Fixed stupid error in the quantitative trait "TDT" (conditional on parental genotypes allelic ANOVA) -- the founder genotypes and phenotypes were not transferred to the work arrays. Linkage locus file now always has N-1 thetas (occasionally would write N, where N is the number of loci).

15-Feb-2000 (0.99.9)

Another equivalence problem fixed, in assoc(), was overwriting allele counts for table (ANOVA results were OK).

14-Feb-2000 (0.99.9)

Minor tweaks to code for allele frequencies. Where all subjects in the dataset are untyped at a marker, they are given a starting genotype of "1/1".

09-Feb-2000 (0.99.9)

Minor changes: if print level is set to 2, tdt also prints out the transmitted and nontransmitted alleles for each informative proband. Use of the he1 command gets the old squared-difference Haseman-Elston regression. A quantitative trait "TDT" added to the output from assoc.

20-Jan-2000 (0.99.9)

Replaced marginal genotypic TDT with simpler one conditioning on parental genotypes. Simulated P-value is now based on typed ancestors of probands (at least both parents). A memory error affecting the IBD matrix for the entire pedigree (wribd) is repaired.

08-Dec-1999 (0.99.8)

Minor bug fixes: greatly increased speed of MC generation of starting genotypes by replacing an inefficient loop.

26-Nov-1999 (0.99.7)

Minor bug fixes - was printing 2*N for the number of genotypes in the pedigree file.

12-Nov-1999 (0.99.7)

Added "gh2" option to write linkage: this adds a dummy trait locus. and writes missing quantitative traits as "-". When added to write locus linkage, it adds the dummy locus and writes the inter-locus distances as centimorgans rather than as recombination fractions. If set tdt first is used, only one proband (both parents typed) in every family is used.

29-Sep-1999 (0.99.7)

Added sibship permutation test for binary trait allelic association analysis. Fixed small bug in ibd estimation for nuclear families.

16-Sep-1999 (0.99.7)

Multilocus IBS sharing calculated for all relative pairs by the share command. This is an unweighted statistic. The expectation and sampling variance are generated by gene-dropping, allowing for the (sex-averaged) linkage map. The results of this may be difficult to interpret -- for example, I surmise they will detect marry-ins from a different ethnic background.

03-Sep-1999 (0.99.7)

Output from Mendelian error checking enhanced slightly -- lists the odd-allele-out in phenoset of an untyped parent causing an inconsistency.

26-Aug-1999 (0.99.6)

Fixed bugs in domix() -- reading wrong data column, and dohist() -- histogram had spurious extra bars.

23-Aug-1999 (0.99.5)

Finally altered sib pair ibd estimation algorithm to use information from all (full-sib) offspring when one or both parents untyped. Half-sib algorithm unchanged. Need to similarly swap over twopoint commands. Fixed bugs in nuclear() -- writing last sibship in each pedigree twice.

12-Aug-1999 (0.99.4)

Minor bugfixes in writing pedigree files (no whitespace between quantitative traits. Added "grandparents" option to nuclear command, so can add if phase information wanted.

05-Jul-1999 (0.99.3)

Adds experimental haplotyping routine (recmin based) and procedure to pinpoint the "lowest common ancestor" of multiple affecteds in a pedigree. The mean marital IBS sharing is now tested versus expectation in the hwe command, and the homozygosity test can also now be applied easily to all typed individuals. Mixtures of normals etc can be fitted to quantitative traits, as can multiple regression analysis. Various Gconvert pedigree and locus file writing routines moved to Sib-pair.

27-Jan-1999 (0.98.9)

Further small bugs removed (mainly printing IDs). The asp command output includes mean IBD sharing for full-sibs, along with the "mean" test P-value (exact binomial two-tailed).

25-Jan-1999 (0.98.8)

Removes two bugs introduced in 0.98.7: one lost every first member of a pedigree (save the first pedigree).

21-Jan-1999 (0.98.7)

This version contains a number of minor improvements, mainly in output from the genotyping error checking routines. Dummy records (and if necessary ID) are now generated for missing parents of nonfounders (that is, where only one parent is specified, or a parent ID is specified but a record for that person was not included). This was previously performed by the auxiliary awk program addpar.awk. Individual IDs can now be alphanumeric. Errors occurring when MAXSIZ, the maximum pedigree size, was increased above 800 have been fixed (these arose from an overflow in the sort key).

28-Aug-1998 (0.98.3)

Fixed bug in algorithm for producing generation numbers: this was adding extra generations when loops were encountered (the pedigree was still correctly sorted in that parents always preceded children. Further tinkering with the MCMC algorithm. This is still not fully correct, as it needs a correct specification of the proposal distribution for the new fsimped() algorithm.

14-Aug-1998 (0.98.2)

Further refinement of MCMC algorithm -- much better handling of multiple marriages by simply replacing the algorithm of genof4() with that used by genof3() -- the latter is used to generate starting genotypes.

21-Jul-1998 (0.97.9)

Implemented "include" command, so commands can be read from an external file. Added ability to select on pedigree size to "select", and to trim nuclear pedigrees to a set size.

2-Jul-1998 (0.97.7)

In Gconvert, fixed problem with "wri loc tcl", which was writing cM, not M. There is an undocumented (save here!) "write locus mim", which writes a header in the appropriate format which can be concatenated onto a Linkage format file. The "keep", "drop" and "undelete" commands now accept ranges eg "drop D1S1 to D1S10".

26-Jun-1998 (0.97.6)

Cleaned up the gener() algorithm so that it correctly assigns generation number when a nominal single pedigree is in fact made up of multiple disjoint pedigrees. The "gener" command now prints out each such subpedigree in turn (if present), and the output is now more compact and easier to read.

16-Jun-1998 (0.97.5)

This adds routines that print out the mean ibd sharing at a marker locus for all pairs of relatives in a pedigree ("ibd"), as well as ("kin") the expected sharing given the degree of relationship (coefficient of relationship), or the inbreeding coefficient. There is also a utility for calculating recurrence risks under SML models ("sml"), and a command ("select") for selecting pedigrees for later analysis based on a trait value of one of its members (very basic). The "write pedigree" command now writes quantitative traits as F9.4, and the martingale residuals output by the "kaplan" command have been changed to those of Therneau et al [1990].

25-May-1998 (0.97.3)

Mainly bug repairs. Both Gconvert and Sib-pair were incorrectly recoding sexes after the "nuclear" procedure (due to change of sex from logical to integer in most but not this routine!). A backslash "\" as the last word on a line now means the next line is a continuation line. The connect() routine in Gconvert now lists all families contained within a disjoint pedigree (ie unrelated individuals with that pedigree ID are present in the pedigree file). Now all printed thetas are positive.

01-Apr-1998 (0.97.2)

Minor bug repairs. Labelling of paternal and maternal genotypes in output from wrgtp() -- list of nuclear family genotypes when inconsistency detected -- was reversed. Stacking of jobs made easier by retaining work and data paths after "clear" issued. Gconvert upgraded to include functions such as "clear", "set data".

13-Mar-1998 (0.97.0)

This version has further changes made to the MCMC algorithm for simulating missing genotypes. The proposals made using fsimped() were not in fact being tested via the Metropolis criterion, as they were being stored in array set() and not array set2(). Again, it seems these changes make little difference to the estimates of ibd in the test pedigrees, although they are noticeable in the joint missing genotype distributions.

03-Mar-1998

Changes the residuals output by the "kap" procedure to the Nelson-Aalen "martingale residuals" described by Commenge from "survivor residuals" based on the product-limit estimator.

02-Mar-1998 (0.96.5)

This adds association analysis for a quantitative trait, implemented as a permutation test ANOVA. A new command "kap" gives the Kaplan-Meier estimate of the survivor function for a binary trait with variable age of onset. The residuals from this analysis can be saved for Haseman-Elston linkage and association analysis.

The Monte-Carlo Markov Chain algorithm for simulating missing genotypes has been further tinkered with, following problems encountered in multigeneration pedigrees where multiple consecutive generations are untyped. I have reintroduced a "switch of origins" operation for heterozygote children of untyped x untyped matings, as the existing "mutation" operation will shuffle such parental genotypes only when the child has no offspring (a fact that had eluded me until now). This seems to fix the trouble. Reanalysis of the example datasets included with Sib-pair found little difference in ibd based statistics compared to the old algorithms. Using the Lange-Goradia algorithm for producing starting genotypes for MCMC can still fail, as described in the original 1987 paper, when loops are present. If this occurs, Sib-pair now switches to its alternative gene-dropping based algorithm.

11-Feb-1998 (0.96.0)

The internal (and outputted) sorting of pedigree members is now by (founder/nonfounder) (generation) (father ID) (mother ID) (ID). This fixes a problem in some pedigrees (thanks to Hank Juo) where starting genotypes for the MCMC algorithms could not be generated via the Lange-Goradia approach. It did not affect the other MC-based approach used when imputation was "off". Since the sort key is currently integer*4, the family size in this new program is limited to approximately 1290.

A "set burn-in" option has been added to allow specification of the number of iterations of the MCMC algorithms to be run prior to the iterations used to calculate statistics. Previously, this was set to zero. In the empirical tests I had done, the Lange-Goradia algorithm generated starting genotypes seemed to give unbiased results, and so I had removed the burn-in. More recently, I have found example families (with missing genotypes) where estimated ibd is biased upwards. This bias is reduced by a suitable number of burn-in iterations.

28-Jan-1998 (0.95.6)

Generate workfile names using time as seed, to avoid clashes on multitasking systems. The "sta" command added. Further work on allpair: "all <tra> wpc" calculates an experimental variant of the randomization weighted-pairwise-statistic of Commenges (see Genet Epidemiol 1997;14:971-4). Further prettification of Gconvert output.

23-Jan-1998 (0.95.5)

Some prettification of Gconvert output.

13-Jan-1998

Added a "set map" command to Gconvert so that the ASPEX and LINKAGE locus files can have a sex-averaged linkage map specified. Maps can also be specified by "set dist" to give intermarker map distances, and by adding a map position at the end of the "set loc" line for a marker.

12-Jan-1998 (0.95.4)

Added ASPEX locus file and GDA pedigree file output to Gconvert. ASPEX reads command files in TCL containing the marker names and intermarker recombination distances (set to 0.50 Morgans by Gconvert). Analysis is set to be of a Linkage format pedigree file containing one binary trait and all the available marker loci. GDA reads an extension of the Nexus format. Gconvert will only write out founders unless told otherwise, as GDA is designed for population genetic work. The likelihood ratios for the IBD based ASP analysis are now corrected back (!) to be twice their former values. The HWE chi-square has been changed to a LR chi-square, to make it more robust in sparse tables. Individual IDs are now written without leading zeroes in most cases, so person 112-00000001 is now written 112-1. A "time" command will give the time elapsed since the program started, or since "time" was last called.

11-Dec-1997

The error in the loop accumulating grandparent-grandchild pairs was present for the parent-offspring pair test as well.

10-Dec-1997 (0.95.3)

Family correlations and recurrence risks now include all pairs regardless of id numbering (the old version would miss grandparent-grandchild pairs where the grandchild ID number was higher than that of the grandparent AND the grandparent was a nonfounder). The "fre[quency]" command now has a synonym "des[criptive]", and can be applied to a single quantitative trait. Previously, the correlations, sibship variance test etc were only available via a global "fre" command. The "und[elete]" command now has a default of returning all deleted loci back to the analysis.

02-Dec-1997

Reformatted apm output (list of affecteds and unaffecteds now after family summary statistics when plevel=1). Ascertainment corrected segregation ratios and standard errors default to those for complete ascertainment (reducing to those of Li & Mantel) if no variable corresponding to proband status is defined (same as "davie trait trait").

26-Nov-1997

Now trims long locus names (>10 characters) when parsing "drop", "keep" and "undelete" commands to correctly match. Does not check for names different at greater than 10th character.

25-Nov-1997 (0.95.2)

Repaired a bug in the "trans" command (boxcox()). If genotypes preceded a quantitative phenotype in a pedigree record, the wrong column would be transformed.

19-Nov-1997 (0.95.1)

Repaired annoying bug in Haseman-Elston regression analysis. Function for calculating ibd-sharing was treating the starting genotypes used for MCMC as if these were observed (therefore does not affect versions prior to 0.93). Never a problem for Gconvert's wrsib command.

Elapsed time now measured by time(), rather than secnds() for DOS version. A refinement only of interest for overnight runs.

Program now warns if there are fewer fields for a pedigree record than expected -- previously these were silently padded out as missing. It still silently ignores extra fields.

Memory utilisation decreased by equivalencing several work arrays.

13-Nov-1997 (0.95.0)

Allowable whitespace in pedigree and control files now includes tabs. Shell commands are echoed as a comment (self documenting calls to other programs).

06-Nov-1997

Fixed bug where multiple drop/keep/undelete statements clashed. Removed punctuation stripping from parser "();". These were originally present so that GAS type control files could be used as a template without editing.

05-Nov-1997

Gconvert now writes an additional line to the dummy description in an outputted LINKAGE style locus file (the variance multiplier), and sets quantitative trait zero values to 0.0001, so they are not treated as missing by LINKAGE.

24-Oct-1997

Summary of MC P-values for APM is now done using an inverse Z transform of the P-value for each pedigree. fval() now reads "y" and "n" as 2.0 and 1.0, making transformation/recoding more transparent.

25-Sep-1997

Repaired bug which made ibs affected half-sib pair chi-square incorrect for sparse tables (few pairs), by changing from Pearson to LR chi-square. Improved gener() algorithm so marry-in generation numbers correct in the presence of loops. DOS executable now a compressed version (using DJP), reducing the size of the file by half.

21-Aug-1997

Repaired bug which meant that the "generation" command only worked if it was the first command after "run". Updated on-line help.

20-Aug-1997

Implemented routine to compare marker homozygosity in probands to that expected based on the sample allele frequencies.

11-Aug-1997

Added keywords "mat" and "pat" to perform TDT analyses only on the contributions of the mother or father of the proband.

06-Aug-1997

Updated Gconvert by adding help, setting all keywords to 3 letter minimum.

03-Aug-1997

Implemented exact two-tailed probabilities for single-allele TDT.

16-Jul-1997

Added routine for correcting segregation ratios for ascertainment.

15-Jul-1997

Added routine for testing HWE at all markers.

28-Jun-1997

Added "set tdt bot[h parents]|one [parent]" limiting TDT if requested to cases where both parents typed. Using cases where one parent is untyped can lead to bias, esp for diallelic markers with unequal allele frequencies. Alpha version of allpairs() routine set working.

26-May-1997

Added IBS based ASP analysis to Sib-pair, and an IBS based test for checking if full-sib pairs are not half-sib pairs (or unrelated!) to Gconvert.

06-Mar-1997

Prettified output of describe().

03-Mar-1997 (0.94)

Sib-pair writing out all simulated genotypes regardless of imputation level to pedigree file. Fixed so now only writes all genotypes if imputation level 3. Added "read linkage" to read Linkage-style pedigree files without having to recode zeroes to missing for quantitative traits. DJGPP V2 now used to produce DOS executable.

05-Feb-1997

Fixed up problem with imputation level 3 in Gconvert. This problem long since fixed in Sib-pair. Involved failure to correctly update genotype array in sequential imputation if genotype became fixed as side effect of another target.

Feb-1997

Trialled djgpp v2. Code seems to be slightly slower than v1 equivalent for some examples, but faster in others. Prepared source code for release.

18-Dec-1996 (0.93)

Released Sib-pair with successful MCMC simulation of missing genotypes. Added to the freq command to gives familial correlations and a version of the Fain sibship variance test for a quantitative trait. Included generation command to lists pedigree members by sibship and generation number. Included transform command to transform a quantitative trait.

18-Oct-1996 (0.92)

Cleaned up several bugs involving recoding/downcoding of alleles [only met if multiple recode statements involving the same marker], calculation of P-values for very large values of chi-square statistics [evaluated incorrectly as 1.0 or NaN in some cases], and error checking [would delete pedigree files with errors in the parent field].

Sep-1996

Versions of Sib-pair for ASP analysis following Faraway (1992). GPM ibs algorithms weight improved as Patrick Ward's program allowed calculation of exact result for comparison.

Jul-1996

Changed MC/randomization routines to sequential approach of Besag.

Mar-1996

Various unreleased versions using different MCMC algorithms.

Aug-1995

Moved Lange-Goradia algorithm from using random-access file to entirely in memory. Required moving from MS-Fortran 4.1 to f2c/djgpp for DOS version.

May-1995

Added estimation of sib-pair IBD sharing where one or two untyped parents.

Apr-1995

First code for multiallelic TDT tests. Imputation done only within nuclear families. Input and output code based on earlier PHI program. GAS pedigree file structure chosen as more readable than LINKAGE style (essentially identical).

marker	an autosomal (fully) codominant marker
xmarker	X-linked codominant marker
quantitative	quantitative (or interval or ordinal) trait
affection	binary trait

write locus	aspex\|tcl	<locus file name>
	fisher
	gas
	linkage\|gh		[dummy]
	loki
	mendel
	merlin
	sage
	sib-pair

SIB-PAIR 0.99.9 (27 May 2003)

by

David L. Duffy

(1995-2003)

A program for elementary genetical analyses

CONTENTS

An example of use

Analytic Methods

Monte Carlo Algorithms

Global commands

Algebraic operators and functions

Data Declaration commands

Analysis and data manipulation commands

ACKNOWLEDGEMENTS

26-May-2003 (0.99.9)

24-April-2003 (0.99.9)

17-April-2003 (0.99.9)

10-April-2003 (0.99.9)

09-April-2003 (0.99.9)

28-March-2003 (0.99.9)

20-March-2003 (0.99.9)

28-February-2003 (0.99.9)

12-February-2003 (0.99.9)

31-January-2003 (0.99.9)

23-January-2003 (0.99.9)

22-January-2003 (0.99.9)

17-January-2003 (0.99.9)

04-October-2002 (0.99.9)

18-October-2002 (0.99.9)

17-October-2002 (0.99.9)

4-October-2002 (0.99.9)

25-September-2002 (0.99.9)

18-September-2002 (0.99.9)

29-July-2002 (0.99.9)

01-July-2002 (0.99.9)

26-June-2002 (0.99.9)

20-June-2002 (0.99.9)

19-June-2002 (0.99.9)

12-June-2002 (0.99.9)

28-May-2002 (0.99.9)

17-May-2002 (0.99.9)

17-Apr-2002 (0.99.9)

05-Apr-2002 (0.99.9)

13-Mar-2002 (0.99.9)

12-Mar-2002 (0.99.9)

06-Mar-2002 (0.99.9)

19-Feb-2002 (0.99.9)

18-Feb-2002 (0.99.9)

15-Feb-2002 (0.99.9)

31-Jan-2002 (0.99.9)

23-Jan-2002 (0.99.9)

18-Jan-2002 (0.99.9)

11-Jan-2002 (0.99.9)

3-Jan-2002 (0.99.9)

29-Nov-2001 (0.99.9)

27-Nov-2001 (0.99.9)

26-Nov-2001 (0.99.9)

16-Nov-2001 (0.99.9)

15-Nov-2001 (0.99.9)

02-Nov-2001 (0.99.9)

11-Sep-2001 (0.99.9)

04-Sep-2001 (0.99.9)

21-Aug-2001 (0.99.9)

17-Aug-2001 (0.99.9)

14-Aug-2001 (0.99.9)

18-Jul-2001 (0.99.9)

17-Jul-2001 (0.99.9)

14-Jul-2001 (0.99.9)

10-Jul-2001 (0.99.9)

6-Jul-2001 (0.99.9)

5-Jul-2001 (0.99.9)

28-Jun-2001 (0.99.9)

20-Jun-2001 (0.99.9)

20-Jun-2001 (0.99.9)

19-Jun-2001 (0.99.9)

18-Jun-2001 (0.99.9)

14-Jun-2001 (0.99.9)

8-Jun-2001 (0.99.9)

6-Jun-2001 (0.99.9)

24-May-2001 (0.99.9)