bam2GRanges: Import BAM file into GRanges

In ataudt/aneufinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

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)

ataudt/aneufinder documentation built on April 18, 2023, 4:20 a.m.