| Class | Analysis and data manipulation command |
| Name | apm |
| Arguments | <binary trait>|(<quantitative trait> >|>=|<|<=|==|^= <threshold>) [ibd|ibs] |
Prints APM statistics for all marker loci versus the trait.
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. The latter include contributions from discordant pairs of relatives and concordantly unaffected pairs, and are especially useful when studying Mendelian disorders. The ibs based test can be of interest when testing for allelic association in families.
Example:
>> apm AD
------------------------------------------------
APM for trait " AD" v. all markers
------------------------------------------------
Marker NFams NAff Z-value Asy P Emp P Iters
---------- ------ ------ ---------- ------ ------ ------
D14S52 3 16 -0.2 0.5969 0.5142 500 APM-IBS .
D14S52 3 16 0.2 0.4336 0.3047 500 GPM-IBS .
D14S43 3 16 3.8 0.0001 0.0014 500 APM-IBS ***
D14S43 3 16 3.4 0.0003 0.0240 500 GPM-IBS **
D14S53 3 15 0.7 0.2507 0.1802 500 APM-IBS .
D14S53 3 15 2.8 0.0024 0.0115 500 GPM-IBS *
>> apm AD ibd
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APM for trait " AD" v. all markers
------------------------------------------------
NOTE: Identity-by-descent based statistic used.
Marker NFams NAff Z-value Asy P Emp P Iters
---------- ------ ------ ---------- ------ ------ ------
D14S52 3 30 0.7 0.2505 0.1960 500 APM-IBD .
D14S52 3 30 1.4 0.0834 0.1004 500 GPM-IBD +
D14S43 3 31 2.2 0.0138 0.0160 500 APM-IBD +
D14S43 3 31 3.1 0.0008 0.0100 500 GPM-IBD **
D14S53 3 30 0.8 0.2199 0.1863 500 APM-IBD .
D14S53 3 30 1.0 0.1559 0.0632 500 GPM-IBD +
>> set ple 1
>> apm AD
------------------------------------------------
APM for trait " AD" v. all markers
------------------------------------------------
----------- APM analysis for "D14S43" --------------
Overall statistics T NFam Asy-P InvZ-P
Aff-Aff
f(p) = 1 4.087 3 0.0000 0.0011
f(p) = 1/sqrt(p) 3.707 3 0.0001 0.0009
f(p) = 1/p 1.743 3 0.0406 0.0137
Aff-UnA
f(p) = 1 -1.184 2 0.1182 0.0991
f(p) = 1/sqrt(p) -1.734 2 0.0414 0.0627
f(p) = 1/p -1.345 2 0.0893 0.0279
Aff-Aff v. Aff-UnA
f(p) = 1 7.263 3 0.0000 0.0013
f(p) = 1/sqrt(p) 5.841 3 0.0000 0.0032
f(p) = 1/p 2.729 3 0.0032 0.0162
GPM
f(p) = 1 4.094 3 0.0000 0.0296
f(p) = 1/sqrt(p) 3.362 3 0.0004 0.0133
f(p) = 1/p 1.987 3 0.0235 0.0320
Total of 16 affecteds and 5 unaffecteds used.
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