daskelly/fstprobs: Read and Write 3D Genoprobs Quickly

This is an experimental package that is designed for facilitating interactive work with large genotype probability matrices, e.g. those used for qtl mapping with the qtl2 or DOQTL R packages. We start with a 3D matrix of dimension n.samples * n.haplotypes * n.markers, and provide functions to write these data (quickly) to disk, and to read in the data (quickly). The fast read/write is achieved using the fst package. Currently works only with DO/CC-style genoprobs with 8 founders, although this dependency is just a sanity check that dim(probs)[2] == 8. *** This package is pretty useless as the speedup is minimal compared to loading RData, but it was a good exercise! ***

Getting started

Package details

Maintainer
LicenseMIT
Version0.0.0.9000
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("daskelly/fstprobs")
daskelly/fstprobs documentation built on July 27, 2018, 12:51 a.m.