R/qtl2 (aka qtl2) is a reimplementation of the QTL analysis software R/qtl, to better handle high-dimensional data and complex cross designs.
It was previously split into the multiple packages qtl2geno, qtl2scan, qtl2plot, and qtl2db, but that proved awkward and confusing and so the packages have been combined. But also see the related package, qtl2convert, for converting data among the R/qtl2, DOQTL, and R/qtl formats. qtl2convert will remain a separate package.
R/qtl2 is not yet available on CRAN, but it can be installed from a mini-CRAN at rqtl.org. Make sure you have the latest version of R.
install.packages("qtl2", repos="http://rqtl.org/qtl2cran")
Alternatively, you can install R/qtl2 from its source on GitHub. (But note that compiling the C++ code can be rather slow.)
On Windows, you'll need Rtools.
On Mac OS X, you'll need the command-line developer tools.
You then need to install the devtools package, plus a set of package dependencies: yaml, jsonlite, data.table, RcppEigen, RSQLite, and qtl. (Additional, secondary dependencies will also be installed.)
install.packages(c("devtools", "yaml", "jsonlite", "data.table", "RcppEigen", "RSQLite", "qtl"))
Finally, install R/qtl2 using devtools::install_github().
library(devtools)
install_github("rqtl/qtl2")
- user guide
- input file formats (see also the sample data files and the qtl2data repository)
- preparing DO mouse data for R/qtl2
- differences between R/qtl and R/qtl2
- developer guide
- HMM benchmarks
To cite R/qtl2 in publications, use:
Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Sen Ś, Yandell BS, Churchill GA (2018) R/qtl2: software for mapping quantitative trait loci with high-dimensional data and multi-parent populations. bioRxiv doi:10.1101/414748