bed2GRanges: Import BED file into GRanges
In AneuFinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Description Usage Arguments Value Examples

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

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

`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=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.

A GRanges-class object containing the reads.

## 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)