readBedFileAsGRanges {chromstaR} | R Documentation

## Import BED file into GRanges

### Description

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

### Usage

    readBedFileAsGRanges(
      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-6 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=0` 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", "liver-H3K4me3-BN-male-bio2-tech1.bed.gz",
                           package="chromstaRData")
    ## Read the file into a GRanges object
    data(rn4_chrominfo)
    reads <- readBedFileAsGRanges(bedfile, assembly=rn4_chrominfo, chromosomes='chr12',
                        min.mapq=10, remove.duplicate.reads=TRUE)
    print(reads)

[Package chromstaR version 1.18.0 Index]