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

In gkeele/miqtl: Suite of QTL Mapping Functions

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

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,
  physical_dist.is.Mb = TRUE,
  map.locus_name.colname = "SNP_ID",
  map.chr.colname = "Chr",
  map.physical_dist.colname = "Mb_NCBI38",
  map.genetic_dist.colname = "cM",
  HAPPY.output.path,
  allele.labels = NULL,
  chr = c(1:19, "X"),
  in.log.scale = FALSE,
  founder.probs.Rdata.available = TRUE,
  samples = NULL,
  simple.alleles = NULL
)

Arguments

DOQTL.recon.output.path	The path to the directory containing DO-QTL founder haplotype output files.
map	The map file (which contains important information on the loci) loaded into R.
physical_dist.is.Mb	DEFAULT: TRUE. IF true, Mb will be converted to bp within the function.
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.
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.
in.log.scale	DEFAULT: FALSE. If TRUE, probabilities are assumed to be log(p-value). Output in genomecache is p-value.
samples	DEFAULT: NULL. If founder.probs.Rdata is not available, input a vector with the DO identifiers. Can be pulled from individual-level files with naming scheme [sample].genotype.probs.Rdata.
simple.alleles	DEFAULT: NULL. If founder.probs.Rdata is not available, input a vector with the simple allele labels. Standard is LETTERS[1:8].

Examples

convert.DOQTL.to.HAPPY()

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