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

In HLindsay/CrispRVariants: Tools for counting and visualising mutations in a target location

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

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

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.