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"))
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. |
This function requires a functioning bedtools installation! See:
- https://github.com/arq5x/bedtools2
- https://bedtools.readthedocs.io/
Updated S3 EIGENSTRAT data object.
## 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)
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