ezScanBam: Scans a bam file

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

Scans a bam file

Description

Scans a bam file with the option to select only a part of the output.

Usage

ezScanBam(
  bamFile,
  seqname = NULL,
  start = NULL,
  end = NULL,
  strand = "*",
  tag = character(0),
  what = scanBamWhat(),
  isFirstMateRead = NA,
  isSecondMateRead = NA,
  isUnmappedQuery = FALSE,
  isProperPair = NA,
  isSecondaryAlignment = NA,
  isDuplicate = NA,
  countOnly = FALSE
)

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().
isFirstMateRead	passed further to scanBamFlag().
isSecondMateRead	passed further to scanBamFlag().
isUnmappedQuery	passed further to scanBamFlag().
isProperPair	passed further to scanBamFlag().
countOnly	a logical specifying whether only counts should be returned or the whole scan of the bam file.

Value

Returns a list representing a scanned bam file.

Author(s)

Rehrauer, Hubert

Schmid, Peter

See Also

scanBam

ScanBamParam

Examples

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

uzh/ezRun documentation built on May 9, 2024, 6:16 p.m.