fst_restore: Restore fst_genoprob object to original dimensions.

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

Restore fst_genoprob object to original dimensions.

Description

Any "fst_genoprob" object has embedded its original data and dimensions. This resets elements ind, chr and mar to the full set.

Usage

fst_restore(object)

fst_genoprob_restore(object)

Arguments

object

Object of class "fst_genoprob" as produced by fst_genoprob().

Details

Object is unclassed and elements ind, chr and mar are changed before reseting attributes as "fst_genoprob" object. See fst_genoprob() for details on the object.

Value

Input object with dimensions restored.

Functions

• fst_genoprob_restore: Deprecated version (to be removed).

See Also

fst_genoprob(), fst_extract()

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)

# subset probabilities
fprobs2 <- subset(fprobs, chr=1:2)

# use object to get the full probabilities back
fprobs5 <- fst_restore(fprobs2)

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

kbroman/qtl2fst documentation built on May 3, 2023, 11:12 a.m.