add_blup_to_lod_peaks: Given a table of LOD peaks and the data used to generate...

In churchill-lab/qtl2tricks: Tricks for Karl Broman's qtl2.

Description

Given a table of LOD peaks and the data used to generate them, calculate the founder allele effects for each peak.

Usage

add_blup_to_lod_peaks(lod.peaks, genoprobs, pheno, K, addcovar, map)

Arguments

lod.peaks	data.frame containing at least 3 columns named annot.id, marker.id and lod. We used annot.id to find the phenotype in expr and marker.id to find the genoprobs at the QTL.
genoprobs	list of 3 dimensional arrays that contain the allele probabilities for the mice. In qtl2 format.
pheno	matrix of phenotypes with samples in rows and phenotypes in columns. In qtl2 format.
K	list of numeric kinship matrices.
addcovar	numeric matrix of additive covariates, created using model.matrix.
map	list of numeric vectors containing marker locations in qtl2 format.

Value

data.frame containing the lod.peaks with the eight founder alleles, in columns A through H, appended.

churchill-lab/qtl2tricks documentation built on May 20, 2019, 1:13 p.m.