admixr (version 0.9.1)

filter_bed: Filter EIGENSTRAT data based on a given BED file

Description

Keep (or discard) SNPs that overlap (or lie outside of) regions in a given BED file.

Usage

filter_bed(data, bed, remove = FALSE, outfile = tempfile(fileext = ".snp"))

Arguments

data

EIGENSTRAT data object.

bed

Path to a BED file.

remove

Remove sites falling inside the BED file regions? By default, sites that do not overlap BED regions are removed.

outfile

Path to an output snp file with coordinates of excluded sites.

Value

Updated S3 EIGENSTRAT data object.

Details

This function requires a functioning bedtools installation! See:

- https://github.com/arq5x/bedtools2

- https://bedtools.readthedocs.io/

Examples

# NOT RUN {
# download an example genomic data set
prefix <- download_data(dirname = tempdir())
# create an EIGENSTRAT R object from the downloaded data
snps <- eigenstrat(prefix)

# get the path to an example BED file
bed <- file.path(dirname(prefix), "regions.bed")

# BED file contains regions to keep in an analysis
snps_kept <- filter_bed(snps, bed)
# BED file contains regions to remove from an analysis
snps_removed <- filter_bed(snps, bed, remove = TRUE)
# }
# NOT RUN {
# }