readBamFileAsGRanges: Import BAM file into GRanges

In chromstaR: Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

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)

chromstaR documentation built on Nov. 8, 2020, 8:29 p.m.