Database Storage of Genotype Probabilities for QTL Mapping

Uses the 'fst' package to store genotype probabilities on disk for the 'qtl2' package. These genotype probabilities are a central data object for mapping quantitative trait loci (QTL), but they can be quite large. The facilities in this package enable the genotype probabilities to be stored on disk, leading to reduced memory usage with only a modest increase in computation time.

qtl2fst

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 modeled after the qtl2feather package which stores files in the feather format.

Installation

Install R/qtl2fst from CRAN:

install.packages("qtl2fst")

Alternatively, install it from R universe:

install.packages("qtl2fst", 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/qtl2fst", build_vignettes=TRUE)

Vignette

View the qtl2fst user guide, available online and also within R:

vignette("qtl2fst", package="qtl2fst")

License

Licensed under GPL-3.