gkeele/kqtl: Suite of QTL Mapping Functions

This package contains a number of useful QTL mapping utilities. It supports single locus modeling in terms of haplotype descent and SNPs. These methods make use of a genome cache directory that contains information on haplotype descent for all individuals at all loci in a specific file setup. For haplotypes, both regression-on-probabilities (ROP) and multiple imputations are possible. For SNPs, dosages (imputation from haplotypes - in the human GWAS sense) are used. An invertible relationship matrix can be used to include a random effect. Exact and approximate (estimation of variance components only under the null model) anlysis are possible. For haplotype analysis, weights can be included on the error covariance matrix.

install.packages("remotes")
remotes::install_github("gkeele/kqtl")