R/qtl2

Karl Broman

R/qtl2 (aka qtl2) is a reimplementation of the QTL analysis software R/qtl, to better handle high-dimensional data and complex cross designs.

Also see the related packages, qtl2convert (for converting data among the R/qtl2, DOQTL, and R/qtl formats), qtl2fst (for storing genotype probabilities on disk), and qtl2ggplot (for ggplot2-based data visualizations).

Installation

Install R/qtl2 from CRAN:

install.packages("qtl2")

Alternatively, install it from R universe:

install.packages("qtl2", repos=c("https://rqtl.r-universe.dev",
                                 "https://cloud.r-project.org"))

Or use remotes to install it from its GitHub source:

install.packages("remotes")
remotes::install_github("rqtl/qtl2")

Documentation

• user guide
• categorized list of functions in R/qtl2
• input file formats (also see the sample data files and the qtl2data repository)
• using qtl2fst for on-disk genotype probabilities
• preparing diversity outbred mouse data for R/qtl2
• resources for mouse genome build GRCm39
• genotype diagnostics for diversity outbred mice
• identifying sample mix-ups in diversity outbred mice
• differences between R/qtl and R/qtl2
• developer guide
• HMM benchmarks
• Tutorial on R/qtl2 by Susan McClatchy and Dan Gatti

Citation

To cite R/qtl2 in publications, use:

Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Sen Ś, Yandell BS, Churchill GA (2019) R/qtl2: software for mapping quantitative trait loci with high-dimensional data and multi-parent populations. Genetics 211:495-502 doi:10.1534/genetics.118.301595

License

Licensed under GPL-3.