qtl2fst (version 0.30)

fst_genoprob: Store genotype probabilities in fst database

Description

Save an R/qtl2 genotype probabilities object to a set of fst files for fast access with reduced memory usage.

Usage

fst_genoprob(
  genoprob,
  fbase,
  fdir = ".",
  compress = 0,
  verbose = TRUE,
  overwrite = FALSE,
  quiet = !verbose
)

Value

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.

Arguments

genoprob

Object of class "calc_genoprob". For details, see the R/qtl2 developer guide and qtl2::calc_genoprob().

fbase

Base of filename for fst database.

fdir

Directory for fst database.

compress

Amount of compression to use (value in the range 0-100; lower values mean larger file sizes)

verbose

Opposite of quiet; deprecated argument (to be removed).

overwrite

If FALSE (the default), refuse to overwrite any files that already exist.

quiet

If FALSE (the default), show messages about fst database creation.

Functions

• fst_genoprob(): Deprecated version (to be deleted)

Details

The genotype probabilities are stored in separate databases for each chromosome as tables of (indivduals*genotypes) x (positions) in directory fst. The dim, dimnames and is_x_chr elements of the object have information about the entire fst database. If a fst_genoprob object is a subset of another such object, the chr, ind, and mar contain information about what is in the subset. However, the fst databases are not altered in a subset, and can be restored by fst_restore(). The actual elements of an "fst_genoprob" object are only accessible to the user after a call to unclass(); instead the usual access to elements of the object invoke subset.fst_genoprob().

See Also

fst_path(), fst_extract(), fst_files(), replace_path(), fst_restore()

Examples

library(qtl2)
grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2"))
map <- insert_pseudomarkers(grav2$gmap, step=1)
probs <- calc_genoprob(grav2, map, error_prob=0.002)
dir <- tempdir()
fprobs <- fst_genoprob(probs, "grav2", dir, overwrite=TRUE)

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