filter_bed: Filter EIGENSTRAT data based on a given BED file

In bodkan/admixr: An Interface for Running 'ADMIXTOOLS' Analyses

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"),
  bedtools_args = ""
)

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.
bedtools_args	Optional arguments to 'bedtools intersect' such as "-sorted" or "-sorted -nonamecheck".

Details

This function requires a functioning bedtools installation! See:

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

- https://bedtools.readthedocs.io/

Value

Updated S3 EIGENSTRAT data object.

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)

## End(Not run)

bodkan/admixr documentation built on Feb. 20, 2025, 4:45 p.m.