bam2GRanges: Import BAM file into GRanges
In daewoooo/primatR: What the Package Does (TODO)

bam2GRanges

R Documentation

Import BAM file into GRanges

Description

Import aligned reads from a BAM file into a GRanges object.

Usage

bam2GRanges(
  bamfile,
  bamindex = bamfile,
  region = NULL,
  pairedEndReads = FALSE,
  remove.duplicate.reads = TRUE,
  min.mapq = 10,
  filterAltAlign = TRUE
)

Arguments

`bamfile`	Bamfile with aligned reads.
`bamindex`	Bam-index file with or without the .bai ending. If this file does not exist it will be created and a warning is issued.
`region`	If only a subset of the genomic regions should be loaded.
`pairedEndReads`	Set to `TRUE` if you have paired-end reads in your file.
`remove.duplicate.reads`	A logical indicating whether or not duplicate reads should be kept.
`min.mapq`	Minimum mapping quality when importing from BAM files.
`filterAltAlign`	Set to `TRUE` if you want to filter out reads with alternative mapping location.