GWAS.by.GLM: Perform GWA by GLM using PCs and/or Other Covariates

In wcrump/GWAS.GLM: Perform GWAS by GLM

Description

Perform GWA by GLM using PCs and/or Other Covariates

Usage

GWAS.by.GLM(gen.data, phen.data, gen.map, covs, corr.thresh, PCs)

Arguments

gen.data	A numeric genotype matrix/data.frame (rows = taxa, columns = markers).
phen.data	A phenotype matrix/data.frame (rows = taxa, column = trait scores). Only one trait is permitted.
gen.map	A matrix/data.frame of SNP information (rows = SNPs, columns = c(SNP_ID, Chromosome, Position))
covs	A matrix/data.frame of covariates (rows = taxa, columns = covariates)
corr.thresh	A numerical value (0-1) indicating the maximum allowed correlation between any one covariate and any one PC
PCs	A numerical value indicating the number of PCs to be included in the GLM equation as additional covariates to any supplied by the user

Value

A vector of p values. Each p value corresponding to one SNP tested.

wcrump/GWAS.GLM documentation built on March 30, 2020, 3:17 a.m.