genoprob_to_alleleprob_fst: Convert genotype probabilities to allele probabilities and...

In kbroman/qtl2fst: Database Storage of Genotype Probabilities for QTL Mapping

Convert genotype probabilities to allele probabilities and write to fst database

Description

Reduce genotype probabilities (as calculated by qtl2::calc_genoprob()) to allele probabilities, writing them to an fst database.

Usage

genoprob_to_alleleprob_fst(
  probs,
  fbase,
  fdir = ".",
  quiet = TRUE,
  cores = 1,
  compress = 0,
  overwrite = FALSE
)

Arguments

probs	Genotype probabilities, as calculated from qtl2::calc_genoprob().
fbase	Base of filename for fst database.
fdir	Directory for fst database.
quiet	IF FALSE, print progress messages.
cores	Number of CPU cores to use, for parallel calculations. (If 0, use parallel::detectCores().) Alternatively, this can be links to a set of cluster sockets, as produced by parallel::makeCluster().
compress	Amount of compression to use (value in the range 0-100; lower values mean larger file sizes)
overwrite	If FALSE (the default), refuse to overwrite any files that already exist.

Details

This is like calling qtl2::genoprob_to_alleleprob() and then fst_genoprob(), but in a way that hopefully saves memory by doing it one chromosome at a time.

Value

Link to fst database for the probs input with probabilities collapsed to alleles rather than genotypes.

See Also

qtl2::genoprob_to_alleleprob(), fst_genoprob()

Examples

library(qtl2)
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
gmap_w_pmar <- insert_pseudomarkers(iron$gmap, step=1)

# genotype probabilities
fst_dir <- file.path(tempdir(), "iron_genoprob")
dir.create(fst_dir)
probs_fst <- calc_genoprob_fst(iron, "iron", fst_dir, gmap_w_pmar, error_prob=0.002)

# allele probabilities
fst_dir_apr <- file.path(tempdir(), "iron_alleleprob")
dir.create(fst_dir_apr)
aprobs_fst <- genoprob_to_alleleprob_fst(probs_fst, "iron", fst_dir_apr)

# clean up: remove all the files we created
unlink(fst_files(probs_fst))
unlink(fst_files(aprobs_fst))

kbroman/qtl2fst documentation built on Nov. 27, 2024, 12:36 p.m.