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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")

Vignette

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

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

License

Licensed under GPL-3.

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Version

Install

install.packages('qtl2fst')

Monthly Downloads

228

Version

0.30

License

GPL-3

Issues

0

Pull Requests

0

Stars

2

Forks

3

Maintainer

Karl Broman

Last Published

November 23rd, 2024

Functions in qtl2fst (0.30)

rbind.fst_genoprob

Join genotype probabilities for different individuals
fst_path

Path used in fst_genoprob object
genoprob_to_alleleprob_fst

Convert genotype probabilities to allele probabilities and write to fst database
fst_genoprob

Store genotype probabilities in fst database
fst_extract

Extract genotype probabilities from fst database
calc_genoprob_fst

Calculate conditional genotype probabilities and write to fst database
cbind.fst_genoprob

Join genotype probabilities for different chromosomes
fst_files

List files used in fst_genoprob object
replace_path

Replace the path used in fst_genoprob object
subset_fst_genoprob

Subsetting genotype probabilities
fst_restore

Restore fst_genoprob object to original dimensions.
summary.fst_genoprob

Summary of an fst_genoprob object