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Retrieve SNPs overlapping intervals

Source: R/calc_AEI.R
get_overlapping_snps.Rd

This function will find SNPs overlapping supplied intervals using a SNPlocs package. The SNPs can be returned in memory (as GPos objects) or written to disk as a bed-file (optionally compressed).

Usage

get_overlapping_snps(gr, snpDb, output_file = NULL)

Arguments

gr

Intervals to query

snpDb

A reference ot a SNPlocs database

output_file

A path to an output file. If supplied the file can be optionally compressed by including a ".gz" suffix. If not supplied, SNPS will be returned as a GenomicRanges::GPos object

Value

GPos object containing SNPs overlapping supplied genomic intervals

Examples

if (require(SNPlocs.Hsapiens.dbSNP144.GRCh38)) {
    gr <- GRanges(rep("22", 10),
        IRanges(seq(10510077, 10610077, by = 1000)[1:10], width = 250),
        strand = "+"
    )
    get_overlapping_snps(gr, SNPlocs.Hsapiens.dbSNP144.GRCh38)
}
#> UnstitchedGPos object with 1 position and 0 metadata columns:
#>       seqnames       pos strand
#>          <Rle> <integer>  <Rle>
#>   [1]       22  10511116      *
#>   -------
#>   seqinfo: 25 sequences (1 circular) from GRCh38.p2 genome