OverWrite Letters (e.g. SNPs) in an XStringSet
Usage
owl(seq, snps, ...)
# S4 method for class 'XStringSet,GRanges'
owl(seq, snps, alt_col = "ALT", ...)
# S4 method for class 'BSgenome,GRanges'
owl(seq, snps, alt_col = "ALT", names, ...)Arguments
- seq
A BSgenome, DNAStringSet, RNAStringSet or other XStringSet.
- snps
A GRanges object with SNP positions and a column containing the alternate allele
- ...
Passed to
Biostrings::replaceLetterAt()- alt_col
Column name in the mcols element of
snpscontaining the alternate allele- names
Sequence names to operate on
Value
An object of the same class as the original object, but with SNPs inserted at the supplied positions
Details
This is a lower-level function called by transmogrify() and
genomogrify(), but able to be called by the user if needed
Note that when providing a BSgenome object, this will first be coerced to a DNAStringSet which can be time consuming.
Examples
seq <- DNAStringSet(c(chr1 = "AAGC"))
snps <- GRanges("chr1:2")
snps$ALT <- "G"
snps
#> GRanges object with 1 range and 1 metadata column:
#> seqnames ranges strand | ALT
#> <Rle> <IRanges> <Rle> | <character>
#> [1] chr1 2 * | G
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
seq
#> DNAStringSet object of length 1:
#> width seq names
#> [1] 4 AAGC chr1
owl(seq, snps)
#> DNAStringSet object of length 1:
#> width seq names
#> [1] 4 AGGC chr1