Import BED file into GRanges

Description

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

Usage

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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 fetchExtendedChromInfoFromUCSC 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=NULL to keep all reads.

max.fragment.width

Maximum allowed fragment length. This is to filter out erroneously wrong fragments.

blacklist

A GRanges or a bed(.gz) file with blacklisted regions. Reads falling into those regions will be discarded.

Value

A GRanges object containing the reads.

Examples

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## 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)

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