genoprob_to_alleleprob_fst: 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
)

Value

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

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.

Examples

Run this code

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))