BedToGenomicRanges

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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

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BedToGenomicRanges(panelBedFilepath,
                   ampliconColumn,
                   split,
                   doReduce,
                   rangeExtend,
                   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.

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

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