bam2GRanges {AneuFinder} | R Documentation

## Import BAM file into GRanges

### Description

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

### Usage

    bam2GRanges(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=NA` 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 single-cell-sequencing reads
    bamfile <- system.file("extdata", "BB150803_IV_074.bam", package="AneuFinderData")
    ## Read the file into a GRanges object
    reads <- bam2GRanges(bamfile, chromosomes=c(1:19,'X','Y'), pairedEndReads=FALSE,
                        min.mapq=10, remove.duplicate.reads=TRUE)
    print(reads)

[Package AneuFinder version 1.12.1 Index]