Add nucleic acid sequence of regions to metadata column
add_sequence(ranges, genome, name = "sequence")GRanges object
BSgenome object or any other valid input to `Biostrings::getSeq()` (Do `showMethods(Biostrings::getSeq)` to show valid types)
name of metadata column to hold sequence information (default: "sequence"). Note, this will overwrite existing columns without warning if the name already exists.
`ranges` with new metadata column named "sequence" (or another value passed to `name`) holding the DNA or RNA sequence from `genome`
data(example_peaks, package = "memes")
dm.genome <- BSgenome.Dmelanogaster.UCSC.dm3::BSgenome.Dmelanogaster.UCSC.dm3
add_sequence(example_peaks, dm.genome)
#> GRanges object with 10 ranges and 1 metadata column:
#> seqnames ranges strand | sequence
#> <Rle> <IRanges> <Rle> | <character>
#> [1] chr3L 14551117-14551323 * | AACTAAAATAGCAAATAAAA..
#> [2] chr3L 14625651-14625851 * | GCGCAGGCTGAAAAGAATCG..
#> [3] chr3L 14634333-14634597 * | TACCCACGCATCTTCAAAAT..
#> [4] chr3L 14636768-14637044 * | AACTTCCAAGACGTAAGACA..
#> [5] chr3L 14638220-14638449 * | AGCGCTAATAATTAGAAGAC..
#> [6] chr3L 14743289-14743632 * | AAAGTTCCATCACCGAAAAG..
#> [7] chr3L 14755114-14755492 * | ATAACGATTGCTTGGCAGCA..
#> [8] chr3L 14759085-14759603 * | GTTTTTCCATAGATGCGAGT..
#> [9] chr3L 14978519-14978765 * | TATTAACGAAAATTGCATAT..
#> [10] chr3L 15104231-15105654 * | GTGGCCCAGACACCCGTTCA..
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths