convert.DOQTL.to.HAPPY: Takes DO-QTL founder haplotype reconstruction output files...

In gkeele/kqtl: Suite of QTL Mapping Functions

Description

This function produces a HAPPY-format genome cache from DO-QTL founder haplotype reconstruction output files. The main output files of importance are the individual-level files with naming scheme [sample].genotype.probs.Rdata.

Usage

convert.DOQTL.to.HAPPY(DOQTL.recon.output.path, map.path, HAPPY.output.path,
  allele.labels = NULL, chr = c(1:19, "X"))

Arguments

DOQTL.recon.output.path	The path to the directory containing DO-QTL founder haplotype output files.
map.path	The path to the map file. The map file contains data on the loci. It should be a tab-delimited file with columns labeled "marker", "chr", "bp", and "pos". "pos" represents map distance in cM. "bp" should be in bp, not Mb.
HAPPY.output.path	The path to a directory that will be created as the HAPPY-format genome cache.
allele.labels	DEFAULT: NULL. Allows for specification of founder labels different from what is in the DO-QTL output. The DEFAULT of NULL leads to using the labels from the DO-QTL output.
chr	DEFAULT: c(1:19, "X"). Allows for specification of the chromosomes. DEFAULT is all the chromosomes from the mouse.

Examples

convert.DOQTL.to.HAPPY()

gkeele/kqtl documentation built on May 17, 2019, 6:06 a.m.