bed2GRanges: Import BED file into GRanges

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

Import BED file into GRanges

Description

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

Usage

bed2GRanges(bedfile, assembly, chromosomes = NULL,
  remove.duplicate.reads = FALSE, min.mapq = 10,
  max.fragment.width = 1000, blacklist = NULL)

Arguments

bedfile	A file with aligned reads in BED format. The columns have to be c('chromosome','start','end','description','mapq','strand').
assembly	Please see getChromInfoFromUCSC for available assemblies. Only necessary when importing BED files. BAM files are handled automatically. Alternatively a data.frame with columns 'chromosome' and 'length'.
chromosomes	If only a subset of the chromosomes should be imported, specify them here.
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.
blacklist	A GRanges-class or a bed(.gz) file with blacklisted regions. Reads falling into those regions will be discarded.

Value

A GRanges-class object containing the reads.

Examples

## Get an example BED file with single-cell-sequencing reads
bedfile <- system.file("extdata", "KK150311_VI_07.bam.bed.gz", package="AneuFinderData")
## Read the file into a GRanges object
reads <- bed2GRanges(bedfile, assembly='mm10', chromosomes=c(1:19,'X','Y'),
                    min.mapq=10, remove.duplicate.reads=TRUE)
print(reads)

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