Retrieves DNA sequence from GBreaks
or GenomicRanges::GRanges
objects that are
properly related to a BSgenome
package, and aligns them with the
pwalign::pairwiseAlignment()
function.
Usage
pairwiseAlignment(pattern, subject, ...)
# S4 method for class 'GRanges,GRanges'
pairwiseAlignment(pattern, subject, ...)
# S4 method for class 'GBreaks,ANY'
pairwiseAlignment(pattern, subject, ...)
Value
Returns a pwalign::PairwiseAlignments
object.
See also
Other Bioconductor API functions:
GBreaks-class
,
getSeq()
,
range_GBreaks()
,
reverse()
,
subsetByOverlaps_GBreaks()
Examples
Scerevisiae <- BSgenome.Scerevisiae.UCSC.sacCer3::Scerevisiae
# Very arbitrary example
gb <- GBreaks( target = GRanges("chrI: 1-20", seqinfo = seqinfo(Scerevisiae))
, query = GRanges("chrI:21-40", seqinfo = seqinfo(Scerevisiae)))
pairwiseAlignment(gb)
#> Warning: pairwiseAlignment() has moved from Biostrings to the pwalign package, and is
#> formally deprecated in Biostrings >= 2.75.1. Please call
#> pwalign::pairwiseAlignment() to get rid of this warning.
#> Global PairwiseAlignmentsSingleSubject (1 of 1)
#> pattern: C-CACACCACACCCACACACC
#> subject: CACACACCACAC-CACACACC
#> score: 9.653366