readRegionsFromBedFile: Read Genomic Regions from BED File
In podkat: Position-Dependent Kernel Association Test

Description Usage Arguments Details Value Author(s) References See Also Examples

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

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

`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).

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.

a GRanges object

Ulrich Bodenhofer bodenhofer@bioinf.jku.at

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

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

read.table

## 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)