BedToGenomicRanges: BedToGenomicRanges

In CNVPanelizer: Reliable CNV detection in targeted sequencing applications

Description

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

Usage

BedToGenomicRanges(panelBedFilepath,
                   ampliconColumn,
                   split,
                   doReduce,
                   rangeExtend,
                   dropChromossomes,
                   skip)

Arguments

panelBedFilepath	Filepath of the bed file.
ampliconColumn	Number of the column that identifies the gene name in the bed file passed through panelBedFilepath.
split	The character used as separator in the ampliconColumn. It is ";" by default.
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.

Value

A GenomicRanges object containing information about the amplicons described in the bed file.

Author(s)

Thomas Wolf, Cristiano Oliveira

Examples

    bedFilepath <- file.path("someFile.bed")
    ampliconColumn <- 4
    genomicRangesFromBed <- BedToGenomicRanges(bedFilepath, ampliconColumn)

CNVPanelizer documentation built on Nov. 8, 2020, 6:47 p.m.