readBamFileAsGRanges {chromstaR} | R Documentation

## Import BAM file into GRanges

### Description

Import aligned reads from a BAM file into a `GRanges-class` object.

### Usage

    readBamFileAsGRanges(
      bamfile,
      bamindex = bamfile,
      chromosomes = NULL,
      pairedEndReads = FALSE,
      remove.duplicate.reads = FALSE,
      min.mapq = 10,
      max.fragment.width = 1000,
      blacklist = NULL,
      what = "mapq"
    )

### Arguments

`bamfile` | A sorted BAM file.
`bamindex` | BAM index file. Can be specified without the .bai ending. If the index file does not exist it will be created and a warning is issued.
`chromosomes` | If only a subset of the chromosomes should be imported, specify them here.
`pairedEndReads` | Set to `TRUE` if you have paired-end reads in your BAM files (not implemented for BED files).
`remove.duplicate.reads` | A logical indicating whether or not duplicate reads should be removed.
`min.mapq` | Minimum mapping quality when importing from BAM files. Set `min.mapq=0` to keep all reads.
`max.fragment.width` | Maximum allowed fragment length. This is to filter out erroneously wrong fragments due to mapping errors of paired end reads.
`blacklist` | A `GRanges-class` or a bed(.gz) file with blacklisted regions. Reads falling into those regions will be discarded.
`what` | A character vector of fields that are returned. Uses the `Rsamtools::scanBamWhat` function. See `Rsamtools::ScanBamParam` to see what is available.

### Value

A `GRanges-class` object containing the reads.

### Examples

    ## Get an example BAM file with ChIP-seq reads
    bamfile <- system.file("extdata", "euratrans", "lv-H3K4me3-BN-female-bio1-tech1.bam",
                          package="chromstaRData")
    ## Read the file into a GRanges object
    reads <- readBamFileAsGRanges(bamfile, chromosomes='chr12', pairedEndReads=FALSE,
                        min.mapq=10, remove.duplicate.reads=TRUE)
    print(reads)

[Package chromstaR version 1.14.1 Index]