initiate_canonical_databases: initiate_canonical_databases

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

initiate_canonical_databases

Description

Parses data into r list variable

Usage

initiate_canonical_databases(
    cosmic_file = "CosmicCLP_MutantExport.tsv.gz",
    ccle_file = "CCLE_mutations.csv",
    ccle_sample_file = "sample_info.csv",
    ref_gen = "GRCH38"
)

Arguments

cosmic_file	The path to the Cosmic CLP file. The Cosmic file can be obtained from "https://cancer.sanger.ac.uk/cell_lines/download" and should be labeled "CosmicCLP_MutantExport.tsv.gz". Ensure that the right reference genome is used
ccle_file	The path to the ccle DNA genotype data file. It should be labeled "CCLE_mutations.csv". Ensure that the right reference genome is used
ccle_sample_file	The path to the CCLE sample file. It should be labeled "sample_info.csv" containing both the DepMap ID and corresponding cell line name.
ref_gen	Reference genome version

Value

Returns message if parsing process has succeeded

Examples

initiate_canonical_databases(
    cosmic_file = "CosmicCLP_MutantExport.tsv.gz",
    ccle_file = "CCLE_mutations.csv",
    ccle_sample_file = "sample_info.csv",
    ref_gen = "GRCH38"
)

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