prepare_elements_from_BED12: Prepares element coords from a BED12 file

In ActiveDriverWGS: A Driver Discovery Tool for Cancer Whole Genomes

Prepares element coords from a BED12 file

Description

Prepares element coords from a BED12 file

Usage

prepare_elements_from_BED12(fname)

Arguments

fname

The file name of a BED12 file containing the desired elements. For further documentation on the BED12 format, refer to the UCSC website.

Value

A data frame containing the following columns to be used as the input element coords to ActiveDriverWGS

chr

autosomal chromosomes as chr1 to chr22 and sex chromosomes as chrX and chrY

start

the start position of the element in base 0 coordinates (BED format)

end

the end position of the element in base 0 coordinates (BED format)

id

the element identifier - if the element contains multiple segments such as exons, each segment should be a separate row with the segment coordinates and the element identifier as id. Elements can be coding or noncoding such as exons of protein coding genes or active enhancers.

Examples

elements = prepare_elements_from_BED12(system.file("extdata",
"chr17.coding_regions.bed",
package = "ActiveDriverWGS",
mustWork = TRUE))

ActiveDriverWGS documentation built on Sept. 3, 2022, 5:05 p.m.