Retrieves DNA sequence from GBreaks
or GRanges
objects that are
properly related to a BSgenome
package, and aligns them with the
Biostrings::pairwiseAlignment
function.
Usage
pairwiseAlignment(pattern, subject, ...)
# S4 method for GRanges,GRanges
pairwiseAlignment(pattern, subject, ...)
# S4 method for GBreaks,ANY
pairwiseAlignment(pattern, subject, ...)
Arguments
- pattern
A
GBreaks
or aGRanges
object- subject
A
GBreaks
or aGRanges
object- ...
Additional arguments passed to
pairwiseAlignment
.
Value
Returns a Biostrings::PairwiseAlignments
object.
See also
See also the Biostrings::pairwiseAlignment
function.
Other Bioconductor API functions:
GBreaks-class
,
as()
,
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)
#> Global PairwiseAlignmentsSingleSubject (1 of 1)
#> pattern: C-CACACCACACCCACACACC
#> subject: CACACACCACAC-CACACACC
#> score: 9.653366