wash.covar: Erase additive covariates LOD peaks on the LOD curve

In eqtl: Tools for analyzing eQTL experiments: A complementary to Karl Broman's 'qtl' package for genome-wide analysis

Description

Sets LOD curve to 0 for a given region size around cofactors included in CIM.

Usage

wash.covar(scanone,covar,window.size=20)

Arguments

scanone	An object of class scanone. See 'qtl' package manual for scanone function details.
covar	A data frame with columns 'trait', 'chr' and 'cM'. covar\$trait is a character strings vector which specifies the names of the traits. covar\$chr is an integer vector which specifies the number of the chromosome. covar\$cM is a numeric vector which specifies the cofactor position in cM.
window.size	a single numeric value which specifies the size of the region to set at zero LOD.

Details

This function is useful to extract the new QTLs from composite interval mapping results. The artifactual LOD peak value obtained from the cofactors are set at zero LOD. Then the QTLs are defined by using the function define.peak . The cofactors loci are defined in a data frame which can be performed by the function map.peak. In this case, the cofactors will be at the maximum LOD peak location defined within the related peak object.

Value

The input scanone object is returned.

Author(s)

Hamid A. Khalili

See Also

scanone, cim.peak, map.peak

Examples

data(seed10);

out.em <- scanone( seed10, pheno.col=1:5, model='normal', method='hk');
out.peak <- define.peak( out.em, 'all');

covar <- map.peak(out.peak)

out.cem <- cim.peak(seed10,out.peak);
out.cem <- wash.covar(out.cem,covar);

out_composite.peak <- define.peak(out.cem,'all');

eqtl documentation built on May 2, 2019, 5:42 a.m.