Filter EIGENSTRAT data based on a given BED file

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

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".

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

if (FALSE) # download an example genomic data set
prefix <- download_data(dirname = tempdir())
# create an EIGENSTRAT R object from the downloaded data
snps <- eigenstrat(prefix)
#> Error in eval(expr, envir, enclos): object 'prefix' not found

# get the path to an example BED file
bed <- file.path(dirname(prefix), "regions.bed")
#> Error in eval(expr, envir, enclos): object 'prefix' not found

# BED file contains regions to keep in an analysis
snps_kept <- filter_bed(snps, bed)
#> Error in eval(expr, envir, enclos): object 'snps' not found
# BED file contains regions to remove from an analysis
snps_removed <- filter_bed(snps, bed, remove = TRUE)
#> Error in eval(expr, envir, enclos): object 'snps' not found