convert.qtl2.to.HAPPY: Takes qtl2geno founder haplotype reconstruction output files...

In gkeele/miqtl: Suite of QTL Mapping Functions

Takes qtl2geno founder haplotype reconstruction output files and re-formats into a HAPPY genome cache

Description

This function produces a HAPPY-format genome cache from qtl2geno founder haplotype reconstruction output files.

Usage

convert.qtl2.to.HAPPY(
  qtl2.object,
  cross.object,
  HAPPY.output.path,
  allele.labels = LETTERS[1:8],
  chr = c(1:19, "X"),
  diplotype.order = c("qtl2", "DOQTL", "CC")
)

Arguments

qtl2.object	The full probabilities output as a list of 3D arrays from qtl2geno.
cross.object	The cross object that includes map information as well as phenotype and covariate information.
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"). Specifies the chromosomes to include in the cache.
diplotype.order	DEFAULT: "qtl2". Specifies the order the diplotype columns are in. The wrong order will result in incorrect rotation of probabilities into dosages.

Examples

convert.qtl2.to.HAPPY()

gkeele/miqtl documentation built on Sept. 13, 2024, 5:49 a.m.