cbind.fst_genoprob: Join genotype probabilities for different chromosomes

In qtl2fst: Database Storage of Genotype Probabilities for QTL Mapping

Description

Join multiple genotype probability objects, as produced by fst_genoprob() for different individuals.

Usage

## S3 method for class 'fst_genoprob'
cbind(..., fbase = NULL, fdir = NULL, overwrite = FALSE, quiet = FALSE)

Arguments

...	Genotype probability objects as produced by fst_genoprob(). Must have the same set of individuals.
fbase	Base of fileame for fst database. Needed if objects have different fst databases.
fdir	Directory for fst database.
overwrite	If FALSE (the default), refuse to overwrite existing .fst files.
quiet	If TRUE, don't show any messages. Passed to fst_genoprob().

Value

A single genotype probability object.

See Also

rbind.fst_genoprob()

Examples

library(qtl2)
grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2"))
map <- insert_pseudomarkers(grav2$gmap, step=1)
probsA <- calc_genoprob(grav2[1:5,1:2], map, error_prob=0.002)
probsB <- calc_genoprob(grav2[1:5,3:4], map, error_prob=0.002)
dir <- tempdir()
fprobsA <- fst_genoprob(probsA, "exampleAc", dir, overwrite=TRUE)
fprobsB <- fst_genoprob(probsB, "exampleBc", dir, overwrite=TRUE)

# use cbind to combine probabilities for same individuals but different chromosomes
fprobs <- cbind(fprobsA, fprobsB, fbase = "exampleABc", overwrite=TRUE)

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

qtl2fst documentation built on Oct. 7, 2021, 5:09 p.m.