Arguments
pheno
Data frame, containing the sample IDs, phenotype data and covariates.
probs
3D numeric array, containing the genotype probabilities for all samples at each SNP. Dimensions must be samples by states by SNPs and all dimensions must be named.
K
Numeric matrix, containing the kinship between individuals as computed by QTLRel.
addcovar
Numeric matrix containing additive covariates.
intcovar
Numeric matrix containing covariates that interact with the QTL.
snps
Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively.