narrowAlignments: Narrow a set of aligned reads to a target region

Description Usage Arguments Value Author(s) Examples

Description

Aligned reads are narrowed to the target region. In the case of reads with deletions spanning the boundaries of the target, reads are narrowed to the start of the deletion,

Usage

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narrowAlignments(alns, target, ...)

## S4 method for signature 'GAlignments,GRanges'
narrowAlignments(alns, target, ...,
  reverse.complement, minoverlap = NULL, verbose = FALSE,
  clipping.ops = c("S", "H"), match.ops = c("M", "X", "="))

Arguments

alns

A GAlignments object including a metadata column "seq" containing the sequence

target

A GRanges object

...

additional arguments

reverse.complement

Should the aligned reads be reverse complemented?

minoverlap

Minimum overlapping region between alignments and target. If not specified, alignments must span the entire target region. (Default: NULL)

verbose

(Default: FALSE)

clipping.ops

CIGAR operations corresponding to clipping (Default: c("S","H"))

match.ops

CIGAR operations corresponding to a match, i.e. a non-indel position (Default: c("M","X","="))

Value

The narrowed alignments (GAlignments)

Author(s)

Helen Lindsay

Examples

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bam_fname <- system.file("extdata", "gol_F1_clutch_2_embryo_4_s.bam",
                         package = "CrispRVariants")
bam <- GenomicAlignments::readGAlignments(bam_fname, use.names = TRUE)
target <- GenomicRanges::GRanges("18", IRanges::IRanges(4647377, 4647399),
          strand = "+")
narrowAlignments(bam, target, reverse.complement = FALSE)

HLindsay/CrispRVariants documentation built on May 28, 2019, 12:40 p.m.