Get genomic sequences

Extract the sequences of the genomic ranges from a GenomicRanges::GRanges or a GBreaks object.

Usage

getSeq(x, ...)

# S4 method for class 'GRanges'
getSeq(x, ...)

# S4 method for class 'GBreaks'
getSeq(x, ...)

Arguments

x

A GBreaks or a GRanges object.

...

Extra arguments (not used, but present for compatibility).

Value

A Biostrings::DNAStringSet object containing the extracted sequence(s).

See also

See also the Biostrings::getSeq function.

Other Bioconductor API functions: GBreaks-class, pairwiseAlignment(), range_GBreaks(), reverse(), subsetByOverlaps_GBreaks()

Author

Charles Plessy

Examples

Scerevisiae <- BSgenome.Scerevisiae.UCSC.sacCer3::Scerevisiae
getSeq(GRanges("chrI:1-20", seqinfo = seqinfo(Scerevisiae)))
#> DNAStringSet object of length 1:
#>     width seq
#> [1]    20 CCACACCACACCCACACACC