create_bed_file: create_bed_file

In RaikOtto/Younikorn: Identification of cancer cell lines based on their weighted mutational/ variational fingerprint

create_bed_file

Description

Creates BED files from the found and not found annotated mutations

Usage

create_bed_file(
match_t,
vcf_fingerprint,
output_file,
ref_gen,
manual_identifier

)

Arguments

match_t	R table which contains the mutations from the training database for the cancer cell lines
vcf_fingerprint	contains the mutations that are present in the query cancer cell line's vcf file
output_file	Path to output file
ref_gen	Reference genome version
manual_identifier	Manually enter a vector of CL name(s) whose bed files should be created, independently from them passing the detection threshold

Value

Returns a message which indicates if the BED file creation has succeeded

RaikOtto/Younikorn documentation built on Oct. 18, 2022, 1:21 a.m.