Sib-pair Command: varcomp


ClassAnalysis and data manipulation command
Namevarcomp
Arguments <quantitative trait> [ae] [ce] [ace] [ade] [aqe (inline | ibs | <marker 1> + ...<marker N>)] [covariate <covariate trait 1> + ...<covariate trait N>].

Performs MVN variance components analysis for a quantitative trait using all phenotyped individuals. Currently fits ADE, ACE, AQE, AE and CE models. The ae option fits AE and E only, and so forth. Multiple covariates can be included in the fixed effects part of the model via adding the cov keyword and a list of covariates at the end of the command line. Only the first marker locus in the list of covariates 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 AQE variance components linkage analysis routines is usually accessed by the qtl...full command, but is also accessible by varcomp aqe. In the latter case, one specifies a set of markers to be combined to give a multipoint ibd estimate for the QTLs ibd status, or if the ibs modifier is present, then all active markers are used to estimate kinship from average marker ibs. One can also read a lower triangular matrix of ibd's for each pedigree from the command line, using aqe inline.

Example:

>> include aceex.in
>> varcomp sace
#
# Examine effect of including ACE I/D genotype
# including allelic and then genotypic effects
# 
>> varcomp sace covariates aceins
>> lrt
>> varcomp sace aqe aceins 
>> varcomp sace aqe aceins covariates aceins
>> set loc a12 qua
>> set loc a22 qua
>>  a12 = (aceins=="1/2")
>>  a22 = (aceins=="2/2")
>> varcomp sace covariates aceins
>> varcomp sace covariates a12 a22
>> lrt

See also:

qtlpairsibs or pedigree VC linkage
lrt compare last 2 models fitted (mix/VC/GLM/GLMM)
fpmMCMC mixed/SML/finite polygenic


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