This repository contains the R package mpQTL, which you can find published in our paper.
This package can use the unified mixed model framework (also known Q + K model) to detect QTLs in genetically diverse populations. Our innovations include support of all polyploid levels and multiallelic markers (like SSRs or haplotypes).
Our research showed that the multiallelic models of mpQTL are particularly useful if you have a high number of alleles in your population. For example in multiparental populations, polyploid heterozygous populations or breeding programmes. In that case obtaining multiallelic markers (haplotypes) turned out to be more accurate and powerful than classical biparental analyses.
You can install this package using devtools::install_github("alethere/mpqtl")
If you have access to our gitlab and want to install it from there, please contact us for instructions.
You can access the online vignette here.
If you want to access your vignette locally you need to build it on install (this will take some time).
devtools::install_github("https://github.com/alethere/mpqtl", build_vignette = T)
browseVignettes("mpQTL")