calc_genoprob_fst: Calculate conditional genotype probabilities and write to fst...
In qtl2fst: Database Storage of Genotype Probabilities for QTL Mapping

Description Usage Arguments Details Value See Also Examples

Uses a hidden Markov model to calculate the probabilities of the true underlying genotypes given the observed multipoint marker data, with possible allowance for genotyping errors.

calc_genoprob_fst(
  cross,
  fbase,
  fdir = ".",
  map = NULL,
  error_prob = 0.0001,
  map_function = c("haldane", "kosambi", "c-f", "morgan"),
  lowmem = FALSE,
  quiet = TRUE,
  cores = 1,
  compress = 0,
  overwrite = FALSE
)

`cross`	Object of class `"cross2"`. For details, see the R/qtl2 developer guide.
`fbase`	Base of filename for fst database.
`fdir`	Directory for fst database.
`map`	Genetic map of markers. May include pseudomarker locations (that is, locations that are not within the marker genotype data). If NULL, the genetic map in `cross` is used.
`error_prob`	Assumed genotyping error probability
`map_function`	Character string indicating the map function to use to convert genetic distances to recombination fractions.
`lowmem`	If `FALSE`, split individuals into groups with common sex and crossinfo and then precalculate the transition matrices for a chromosome; potentially a lot faster but using more memory.
`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.

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

A list containing the attributes of genoprob and the address for the created fst database. Components are:

dim - List of all dimensions of 3-D arrays.
dimnames - List of all dimension names of 3-D arrays.
is_x_chr - Vector of all is_x_chr attributes.
chr - Vector of (subset of) chromosome names for this object.
ind - Vector of (subset of) individual names for this object.
mar - Vector of (subset of) marker names for this object.
fst - Path and base of file names for the fst database.

qtl2::calc_genoprob(), fst_genoprob()

library(qtl2)
grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2"))
gmap_w_pmar <- insert_pseudomarkers(grav2$gmap, step=1)
fst_dir <- file.path(tempdir(), "grav2_genoprob")
dir.create(fst_dir)
probs_fst <- calc_genoprob_fst(grav2, "grav2", fst_dir, gmap_w_pmar, error_prob=0.002)

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