ezReadGappedAlignments: Reads gapped alignments from bam

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Reads gapped alignments from bam

Description

Reads gapped alignments from a bam file.

Usage

ezReadGappedAlignments(
  bamFile,
  seqname = NULL,
  start = NULL,
  end = NULL,
  strand = "*",
  tag = character(0),
  what = character(0),
  use.names = TRUE,
  isFirstMateRead = NA,
  isSecondMateRead = NA,
  isUnmappedQuery = FALSE,
  isProperPair = NA,
  isSecondaryAlignment = NA,
  minMapQuality = 0,
  tagFilter = list(),
  keepMultiHits = TRUE
)

Arguments

bamFile	a character representing the bam file path.
seqname	an optional character vector to keep only the specified sequence names in the returned reads.
start	an optional integer vector to limit the start position of the range of returned reads.
end	an optional integer vector to limit the start position of the range of returned reads.
strand	a character specifying which strand to use (+, - or *).
tag	passed further to ScanBamParam().
what	passed further to ScanBamParam().
use.names	passed further to readGAlignments().
isFirstMateRead	passed further to scanBamFlag().
isSecondMateRead	passed further to scanBamFlag().
isUnmappedQuery	passed further to scanBamFlag().
isProperPair	passed further to scanBamFlag().
minMapQuality	an integer specifying the minimal mapping quality to use.
keepMultiHits	a logical specifying whether to keep multiple hits.

Value

Returns an object of the class GAlignments.

Author(s)

Rehrauer, Hubert

Schmid, Peter

See Also

scanBam

ScanBamParam

readGAlignments

Examples

bamFile <- system.file("extdata", "ex1.bam", package="Rsamtools", mustWork=TRUE)
ga = ezReadGappedAlignments(bamFile)

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.