browse: Browse QTL results

In rqtl/qtl2browse: Genetics Genome Browser

Description

Use the genetics genome browser to browse QTL mapping results

Usage

browse(scan1output, map, lodcolumn = 1, min_lod = 0, dir = NULL)

Arguments

scan1output	Genome scan output, as from qtl2::scan1()
map	Corresponding physical map (in Mbp), as a list of chromosomes that are each a vector of marker positions. Can also be a data frame of SNP information, with columns chr, pos, and snp_id.
lodcolumn	LOD score column to plot (a numeric index, or a character string for a column name). Only one value allowed.
min_lod	Minimum LOD score to show; values below this are omitted.
dir	Optional directory to contain the results. If not provided, a temporary directory is created.

Value

File location (hidden).

Examples

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)

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