fst_extract: Extract genotype probabilities from fst database
In qtl2fst: Database Storage of Genotype Probabilities for QTL Mapping

Description Usage Arguments Details Value Functions See Also Examples

Extract genotype probabilities from fst database as an ordinary calc_genoprob object.

1
2
3

fst_extract(object)

fst2calc_genoprob(object)

object

Object of class "fst_genoprob", linking to an fst database of genotype probabilities.

The genotype probabilities are extracted from the fst database. Each chromosome is extracted in turn.

An object of class "calc_genoprob" (a list of 3-dimensional arrays).

fst2calc_genoprob: Deprecated version (to be deleted)

fst_genoprob()

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)
nprobs <- fst_extract(fprobs)

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