convert.full.DOQTL.array.to.HAPPY: Takes founder haplotype reconstructions as a 3D array (with...

In gkeele/miqtl: Suite of QTL Mapping Functions

Takes founder haplotype reconstructions as a 3D array (with the 36 probability states as one of the dimensions) and re-formats into a HAPPY-style genome cache

Description

This function produces a HAPPY-format genome cache from a founder haplotype reconstruction 3D array. DO-QTL does not normally output this 3D array, but rather the dosages. However, this function requires the full probabilities, not the dosages.

Usage

convert.full.DOQTL.array.to.HAPPY(
  full.array,
  map,
  map.locus_name.colname = "SNP_ID",
  map.chr.colname = "Chr",
  map.physical_dist.colname = "Mb_NCBI38",
  map.genetic_dist.colname = "cM",
  HAPPY.output.path,
  remove.chr.from.chr = FALSE,
  physical_dist.is.Mb = TRUE,
  allele.labels = LETTERS[1:8],
  chr = c(1:19, "X"),
  diplotype.order = c("DOQTL", "CC", "qtl2")
)

Arguments

full.array	3D array that contains the founder probabilities. Should be dimension n x 36 x p, where n is the number of individuals and p is the number of loci.
map	The map file (which contains important information on the loci) loaded into R.
map.locus_name.colname	DEFAULT: "SNP_ID". The column name in the map data that corresponds to locus/marker names.
map.chr.colname	DEFAULT: "Chr". The column name in the map data that corresponds to chromosome.
map.physical_dist.colname	DEFAULT: "Mb_NCBI38". The column name in the map data that corresponds to physical position.
map.genetic_dist.colname	DEFAULT: "cM". The column name in the map data that corresponds to genetic position.
HAPPY.output.path	The path to a directory that will be created as the HAPPY-format genome cache.
remove.chr.from.chr	DEFAULT: FALSE. Option to remove "chr" from chromosome information. As in, change "chr1" to "1". The function expects chromosome information to not include "chr" as a prefix.
physical_dist.is.Mb	DEFAULT: TRUE. IF true, Mb will be converted to bp within the function.
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.
diplotype.order	DEFAULT: "DOQTL". Specify the order of the diplotypes in the 3D array, so that the rotation to dosages is done correctly.

Examples

convert.full.DOQTL.array.to.HAPPY()

gkeele/miqtl documentation built on June 13, 2022, 4:20 p.m.