BedToGenomicRanges {CNVPanelizer} | R Documentation |
It generates a GenomicRanges object from a bed file. Needs to be passed the correct number of the gene name column. If the strings contain more information then just the gene name, a splitting character (split) has to be defined. I.e GeneName1;Amplicon2
BedToGenomicRanges(panelBedFilepath, ampliconColumn, split, doReduce, rangeExtend, dropChromossomes, skip)
panelBedFilepath |
Filepath of the bed file. |
ampliconColumn |
Number of the column that identifies the gene name in the bed file
passed through |
split |
The character used as separator in the |
doReduce |
Should overlapping ranges be merged. |
rangeExtend |
Should the defined ranges be extended left and right by the given value. Affects the merging of overlapping regions and also read counting. |
dropChromossomes |
Drop chromossomes. |
skip |
How many lines should be skipped from the top of the bed file. The function assumes a bed file with column names. Thus default is skip = 1. |
A GenomicRanges
object containing information about the amplicons
described in the bed file.
Thomas Wolf, Cristiano Oliveira
bedFilepath <- file.path("someFile.bed") ampliconColumn <- 4 genomicRangesFromBed <- BedToGenomicRanges(bedFilepath, ampliconColumn)