readBamFile {ATACseqQC} | R Documentation

## read in bam files

### Description

wraper for readGAlignments/readGAlignmentsList to read in bam files.

### Usage

    readBamFile(
      bamFile,
      which,
      tag = character(0),
      what = c("qname", "flag", "mapq", "isize", "seq", "qual", "mrnm"),
      flag = scanBamFlag(isSecondaryAlignment = FALSE, isUnmappedQuery = FALSE,
        isNotPassingQualityControls = FALSE, isSupplementaryAlignment = FALSE),
      asMates = FALSE,
      bigFile = FALSE,
      ...
    )

### Arguments

`bamFile` | character(1). Bam file name.
`which` | A GRanges, IntegerRangesList, or any object that can be coerced to a RangesList, or missing object, from which a IRangesList instance will be constructed. See ScanBamParam.
`tag` | A vector of characters indicates the tag names to be read. See ScanBamParam.
`what` | A character vector naming the fields to return. Fields are described on the Rsamtools[scanBam] help page.
`flag` | An integer(2) vector used to filter reads based on their 'flag' entry.
`asMates` | logical(1). Paired ends or not
`bigFile` | If the file take too much memory, set it to true to avoid read the reads into memory. scanBamFlag helper function.
`...` | parameters used by readGAlignmentsList or readGAlignments

### Value

A GAlignmentsList object when asMates=TRUE, otherwise A GAlignments object. If bigFile is set to TRUE, no reads will be read into memory at this step and empty GAlignments/GAlignmentsList will be returned.

### Author(s)

Jianhong Ou

### Examples

    library(BSgenome.Hsapiens.UCSC.hg19)
    which <- as(seqinfo(Hsapiens)["chr1"], "GRanges")
    bamfile <- system.file("extdata", "GL1.bam",
                           package="ATACseqQC", mustWork=TRUE)
    readBamFile(bamfile, which=which, asMates=TRUE)

[Package ATACseqQC version 1.11.8 Index]