| intra-range-methods {GenomicAlignments} | R Documentation |
This man page documents intra range transformations of a GAlignments or GAlignmentsList object.
See ?`intra-range-methods` and
?`inter-range-methods` in the IRanges
package for a quick introduction to intra range and inter range
transformations.
Intra range methods for GRanges and GRangesList objects are defined and documented in the GenomicRanges package.
## S4 method for signature 'GAlignments' narrow(x, start=NA, end=NA, width=NA, use.names=TRUE) ## S4 method for signature 'GAlignmentsList' narrow(x, start=NA, end=NA, width=NA, use.names=TRUE) ## S4 method for signature 'GAlignments' qnarrow(x, start=NA, end=NA, width=NA) ## S4 method for signature 'GAlignmentsList' qnarrow(x, start=NA, end=NA, width=NA)
x |
A GAlignments or GAlignmentsList object. |
start, end, width |
Vectors of integers.
NAs and negative values are accepted and "solved" according to the
rules of the SEW (Start/End/Width) interface (see
See |
use.names |
See |
()
narrow on a GAlignments object behaves
like on a Ranges object. See
?`intra-range-methods` for the details.
A major difference though is that it returns a GAlignments object instead of a Ranges object.
Unlike with qnarrow (see below), the
start/end/width arguments here describe
the narrowing on the reference side, not the query side.
()
qnarrow on a GAlignments object behaves like narrow
except that the start/end/width arguments here
specify the narrowing with respect to the query sequences.
qnarrow on a GAlignmentsList object
returns a GAlignmentsList object.
An object of the same class as, and parallel to (i.e. same length
and names as), the original object x.
There is no difference between narrow and qnarrow when
all the alignments have a simple CIGAR (i.e. no indels or junctions).
Hervé Pagès and V. Obenchain <Valerie.Obenchain@RoswellPark.org>
GAlignments and GAlignmentsList objects.
The intra-range-methods man page in the IRanges package.
The intra-range-methods man page in the GenomicRanges package.
## ---------------------------------------------------------------------
## A. ON A GAlignments OBJECT
## ---------------------------------------------------------------------
ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
param <- ScanBamParam(what=c("seq", "qual"))
gal <- readGAlignments(ex1_file, param=param)
gal
## This trims 3 nucleotides on the left and 5 nucleotides on the right
## of each alignment:
gal2 <- qnarrow(gal, start=4, end=-6)
gal2
## Note that the 'start' and 'end' values are relative to the query
## sequences and specify the query substring that must be kept for each
## alignment. Negative values are relative to the right end of the query
## sequence.
## Also note that the metadata columns on 'gal' are propagated as-is so
## the "seq" and "qual" matadata columns must be adjusted "by hand" with
## narrow();
mcols(gal2)$seq <- narrow(mcols(gal)$seq, start=4, end=-6)
mcols(gal2)$qual <- narrow(mcols(gal)$qual, start=4, end=-6)
gal2
## Sanity checks:
stopifnot(identical(qwidth(gal2), width(mcols(gal2)$seq)))
stopifnot(identical(qwidth(gal2), width(mcols(gal2)$qual)))
## ---------------------------------------------------------------------
## B. ON A GAlignmentsList OBJECT
## ---------------------------------------------------------------------
gal1 <- GAlignments(
seqnames=Rle(factor(c("chr1", "chr2", "chr1", "chr3")),
c(1, 3, 2, 4)),
pos=1:10, cigar=paste0(10:1, "M"),
strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
names=head(letters, 10), score=1:10)
gal2 <- GAlignments(
seqnames=Rle(factor(c("chr2", "chr4")), c(3, 4)), pos=1:7,
cigar=c("5M", "3M2N3M2N3M", "5M", "10M", "5M1N4M", "8M2N1M", "5M"),
strand=Rle(strand(c("-", "+")), c(4, 3)),
names=tail(letters, 7), score=1:7)
galist <- GAlignmentsList(noGaps=gal1, Gaps=gal2)
galist
qnarrow(galist)