| Class | Analysis and data manipulation command |
| Name | qtlpair |
| 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 |
| << (twopair) | Up to index | >> (linkage) |