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R/qtl2 package using fst to store genotype probabilities
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README.md

qtl2fst

Build Status

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

The qtl2fst package uses the fst package to store genotype probabilities in a set of files for rapid access but reduced memory usage. It is fully integrated with R/qtl2, and is based on the qtl2feather package which stores files in the feather format.


Installation

Make sure you have the latest version of R. Then install R/qtl2 using the following. (For more detail, see the instructions at https://kbroman.org/qtl2.)

install.packages("qtl2", repos="http://rqtl.org/qtl2cran")

Next install the fst, dplyr, and devtools packages.

install.packages(c("fst", "dplyr", "devtools"))

Once you have installed these, install qtl2fst from GitHub:

devtools::install_github("kbroman/qtl2fst")

To also install vignettes, include build_vignettes=TRUE:

devtools::install_github("kbroman/qtl2fst", build_vignettes = TRUE)

License

Licensed under GPL-3.

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