BAM2GenomicRanges {Repitools} | R Documentation

## Read in a (list of) BAM file(s) into a GRanges(List) object.

### Description

A wrapper script for coverting the contents of BAM files for use with `GenomicRanges` classes.

### Usage

      ## S4 method for signature 'character'
    BAM2GRanges(path, what = character(),
          flag = scanBamFlag(isUnmappedQuery = FALSE, isDuplicate = FALSE),
          verbose = TRUE)
      ## S4 method for signature 'character'
    BAM2GRangesList(paths, what = character(),
          flag = scanBamFlag(isUnmappedQuery = FALSE, isDuplicate = FALSE),
          verbose = TRUE)

### Arguments

`path` | A character vector of length 1. The path of the BAM file.
`paths` | A character vector of possibly any length. The paths of the BAM files.
`what` | What optional attributes of a read to retain. See `scanBam` and the `value` section.
`flag` | What kinds of reads to retain. See `ScanBamParam` and the `flag` argument.
`verbose` | Whether to print the progess of processing.

### Value

For the single pathname method; a GRanges object. For the multiple pathnames method; a GRangesList object.

### Author(s)

Dario Strbenac

### Examples

      tiny.BAM <- system.file("extdata", "ex1.bam", package = "Rsamtools")
      if(length(tiny.BAM) > 0)
        print(BAM2GRanges(tiny.BAM))

[Package Repitools version 1.33.3 Index]