intra-range-methods: Intra range transformations of a GAlignments or...

In GenomicAlignments: Representation and manipulation of short genomic alignments

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

## 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)

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.

Details

• () 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 instead of the reference sequences.

  qnarrow on a GAlignmentsList object returns a GAlignmentsList object.

Value

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

Note

There is no difference between narrow and qnarrow when all the alignments have a simple CIGAR (i.e. no indels or junctions).

Author(s)

Hervé Pagès and Valerie Obenchain

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")
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)

GenomicAlignments documentation built on Nov. 8, 2020, 8:12 p.m.