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/
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: object 'prefix' not found
# get the path to an example BED file
bed <- file.path(dirname(prefix), "regions.bed")
#> Error: object 'prefix' not found
# BED file contains regions to keep in an analysis
snps_kept <- filter_bed(snps, bed)
#> Error: object 'snps' not found
# BED file contains regions to remove from an analysis
snps_removed <- filter_bed(snps, bed, remove = TRUE)
#> Error: object 'snps' not found
# \dontrun{}