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), 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. This is most easily created with the
`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. Rsamtools[scanBamFlag] helper function.
`...` | parameters used by readGAlignmentsList or readGAlignments

### Value

A GAlignmentsList object when asMats=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 1.6.4 Index]