GenomicAlignments (version 1.2.2)

intra-range-methods: Intra range transformations of a GAlignments or GAlignmentsList object

Description

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.

Usage

"narrow"(x, start=NA, end=NA, width=NA, use.names=TRUE)
"narrow"(x, start=NA, end=NA, width=NA, use.names=TRUE)
"qnarrow"(x, start=NA, end=NA, width=NA)
"qnarrow"(x, start=NA, end=NA, width=NA)

Arguments

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 ?solveUserSEW for more information about the SEW interface).

See ?`intra-range-methods` for more information about the start, end, and width arguments.

use.names

See ?`intra-range-methods`.

Value

An object of the same class as, and parallel to (i.e. same length and names as), the original object x.

Details

• () 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.

See Also

• GAlignments and GAlignmentsList objects.

• The intra-range-methods man page in the IRanges package.

• The intra-range-methods man page in the GenomicRanges package.

Examples

## ---------------------------------------------------------------------
## A. ON A GAlignments OBJECT
## ---------------------------------------------------------------------
ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
gal <- readGAlignments(ex1_file, param=ScanBamParam(what="flag"))
gal

## This trims 3 nucleotides on the left and 5 nucleotides on the right
## of each alignment:
qnarrow(gal, start=4, end=-6)
## Note that the 'start' and 'end' arguments specify what part of each
## query sequence should be kept (negative values being relative to the
## right end of the query sequence), not what part should be trimmed.

## Trimming on the left doesn't change the "end" of the queries.
qnarrow(gal, start=21)
stopifnot(identical(end(qnarrow(gal, start=21)), end(gal)))

## ---------------------------------------------------------------------
## 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)