vqtl2

Overview

vqtl2 is a drop-in extension of qtl2, providing the functions to accommodate variance heterogeneity arising from background factors and detect vQTL, as described in the literature:

The central functions of package vqtl2 are:

  • scan1var() conducts a genome scan
  • scan1var_perm() conducts permutations to assess the statistical significance of findings
  • plot_scan1var() plots the association statistic(s) at each genetic locus
  • plot_allele_effects() plots the genetic and non-genetic effects at a given locus

These all inter-operate with package qtl and follow most of the same paradigms.

If you are new to QTL mapping, the best place to start is the Karl Broman’s website.

Installation

I plan to put vqtl2 on CRAN, but until then, the easiest way to get vqtl2 is from github. The easiest way to download and install an R package from github is with the devtools package, which is available on CRAN. Here’s the R code to do that:

install.packages('devtools')
devtools::install_github(repo = 'rcorty/vqtl2')

Usage

library(vqtl2)
# todo

Getting help

If you encounter a bug, please post a minimal reproducible example on the github issues page. For notes on how to produce a minimal reproducible example, check out this StackOverflow post.

Please note that the ‘vqtl2’ project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.