Sib-pair Command: qtlpair


ClassAnalysis and data manipulation command
Nameqtlpair
Arguments <quantitative trait> [full] [cqe] [covariate <covariate trait 1>]

Performs variance components linkage analysis for all marker loci versus the trait using full-sib relative pairs, or if the full option is active, all genotyped individuals. Both the polygenic background and the QTL are modelled as additive genetic. Covariates, which can include codominant marker loci, are added using as cov keyword-trait pairs. Only the first marker locus is fully allelic effect coded, with subsequent markers included as the mean of their allele values (i.e. 1="1/1", 1.5="1/2", 2="2/2" for a diallelic marker).

The MCMC ibd algorithm is used for the full analysis, and this automatically gives multipoint estimates for tightly (completely) linked adjacent markers by combining estimates (variance-weighted mean).

Example:

>> include volgaex.in
>> set iter 5000
>> set loc survres qua
>> survres=onset
>> kap survres AD res
#
# Maybe not so appropriate, as the residuals are not 
# nicely distributed
# see "histogram survres"
#
>> qtl survres full

---------------------------------------------------------
VC linkage analysis for trait "survres" v. all markers
---------------------------------------------------------

Marker         NFams  NPheno lod score  Asy P  Emp P  Iters
-------------- ------ ------ ---------- ------ ------ ------
D14S52              3     61        0.6 0.0422 1.0000      0 VC  +
D14S43              3     61        1.3 0.0082 1.0000      0 VC  *
D14S53              3     61        0.7 0.0378 1.0000      0 VC  +

#
# cf
#
>> he1 survres simulate

---------------------------------------------------------
Standard H-E for trait "survres" v. all markers
---------------------------------------------------------

Marker         FSibs  HSibs  t-value    Asy P  Emp P  Iters
-------------- ------ ------ ---------- ------ ------ ------
D14S52             13      0        1.1 0.8512 0.8772     57 H-E .
D14S43             13      0       -2.3 0.0309 0.0034   5001 H-E *
D14S53             10      0       -0.8 0.2270 0.1730    289 H-E .

>> apm AD ibd

------------------------------------------------
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     31        0.6 0.2654 0.1883   5000 APM-IBD .
    D14S52          3     31        1.6 0.0536 0.0666   5000 GPM-IBD +
    D14S43          3     31        3.0 0.0012 0.0019   5000 APM-IBD *
    D14S43          3     31        3.6 0.0002 0.0050   5000 GPM-IBD **
    D14S53          3     29        0.7 0.2375 0.1645   5000 APM-IBD .
    D14S53          3     29        0.8 0.2196 0.1093   5000 GPM-IBD .

See also:

varcomp Variance Components trait analysis
set ibd Threshold for lumping markers for multipoint ibd


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