readRegionsFromBedFile {podkat} | R Documentation

## Read Genomic Regions from BED File

### Description

Reads a BED file and returns the genomic regions as `GRanges` object

### Usage

    readRegionsFromBedFile(file, header=FALSE, sep="\t",
                           col.names=c("chrom", "chromStart",
                                       "chromEnd", "names", "width",
                                       "strand"),
                           ignoreMcols=TRUE, seqInfo=NULL)

### Arguments

`file` | the name of the file, text-mode connection, or URL to read data from
`header,sep,col.names` | arguments passed on to `read.table`
`ignoreMcols` | if `TRUE` (default), further columns are ignored; if `FALSE`, further columns are appended to the resulting `GRanges` object as metadata colums (see details below).
`seqInfo` | can be `NULL` (default) or an object of class `Seqinfo` (see details below).

### Details

This function is a simple wrapper around the `read.table` function that reads from a BED file and returns the genomic regions as a `GRanges` object. How the file is split into columns can be controlled by the arguments `header`, `sep`, and `col.names`. These arguments are passed on to `read.table` as they are. The choice of the `col.names` argument is crucial. A wrong `col.names` argument results in erroneous assignment of columns. The function `readRegionsFromBedFile` requires columns named “chrom”, “chromStart”, and “chromEnd” to be present in the object returned from `read.table` upon reading from the BED file. If a column named “strands” is contained in the BED file, this column is used as strand info in the resulting `GRanges` object.

If `ignoreMcols=TRUE` (default), further columns are ignored. If `ignoreMcols=FALSE`, all columns other than “chrom”, “chromStart”, “chromEnd”, “names”, “strand”, and “width” are appended to the resulting `GRanges` object as metadata columns.

The `seqInfo` argument can be used to assign the right metadata, such as, genome, chromosome names, and chromosome lengths to the resulting `GRanges` object.

### Value

a `GRanges` object

### Author(s)

Ulrich Bodenhofer bodenhofer@bioinf.jku.at

### References

http://www.bioinf.jku.at/software/podkat

http://genome.ucsc.edu/FAQ/FAQformat.html#format1

### See Also

`read.table`

### Examples

    ## basic example (hg38 regions of HBA1 and HBA2)
    bedFile <- system.file("examples/HBA.bed", package="podkat")
    readRegionsFromBedFile(bedFile)

    ## example with enforcing seqinfo
    data(hg38Unmasked)
    readRegionsFromBedFile(bedFile, seqInfo=seqinfo(hg38Unmasked))

    ##
    ## example with regions targeted by Illumina TruSeq Exome Enrichment kit:
    ## download file "truseq_exome_targeted_regions.hg19.bed.chr.gz" from
    ## http://support.illumina.com/downloads/truseq_exome_targeted_regions_bed_file.ilmn
    ## (follow link "TruSeq Exome Targeted Regions BED file"; these regions
    ##  are based on hg19)
    ##
    ## Not run:
    readRegionsFromBedFile("truseq_exome_targeted_regions.hg19.bed.chr.gz")

    data(hg19Unmasked)
    readRegionsFromBedFile("truseq_exome_targeted_regions.hg19.bed.chr.gz",
                           seqInfo=seqinfo(hg19Unmasked))
    ## End(Not run)

[Package podkat version 1.12.0 Index]