README.md

In rqtl/qtl2browse: Genetics Genome Browser

R/qtl2browse

Karl Broman and Christian Fischer

R/qtl2browse is an R package to facilitate the use of the Genetics Genome Browser with R/qtl2.

Installation

Install the package remotes.

install.packages("remotes")

Install R/qtl2browse from GitHub using install_github.

remotes::install_github("rqtl/qtl2browse")

Usage

At present, there is a single function, browse(), which takes genome scan output from qtl2::scan1(), writes it to a JSON file, and opens it in a web browser.

Here's an example using data from Recla et al. (2014) and Logan et al. (2013). The calculations are a bit slow.

library(qtl2)
recla <- read_cross2(paste0("https://raw.githubusercontent.com/rqtl/",
                            "qtl2data/master/DO_Recla/recla.zip"))

gmap <- insert_pseudomarkers(recla$gmap, step=0.2, stepwidth="max")
pmap <- interp_map(gmap, recla$gmap, recla$pmap)
pr <- calc_genoprob(recla, gmap, error_prob=0.002,
                    map_function="c-f", cores=0)
apr <- genoprob_to_alleleprob(pr)

k <- calc_kinship(apr, "loco", cores=0)

out <- scan1(apr, recla$pheno[,"HP_latency"], k, cores=0)

library(qtl2browse)
browse(out, pmap)

License

R/qtl2browse is released under the MIT license, as is the Genetics Genome Browser.

rqtl/qtl2browse documentation built on Jan. 2, 2021, 4:54 p.m.