Uniquorn (version 1.0.8)

add_custom_vcf_to_database: Adds a custom vcf file to the three existing cancer cell line panels

Description

Adds a custom vcf file to the three existing cancer cell line panels

Usage

add_custom_vcf_to_database(  vcf_file_path, 
ref_gen = "GRCH37", 
name_cl = "", 
safe_mode = FALSE, 
test_mode = FALSE)

Arguments

vcf_file_path

Input vcf file. Only one sample column allowed.

ref_gen

Reference genome version. All training sets are associated with a reference genome version. Default: GRCH37

name_cl

Name of the to-be-added cancer cell line sample. '_CUSTOM' will automatically be added as suffix.

safe_mode

Only add mutations to the database where there already are mutations found in the cannonical cancer cell lines. This is a safety mechanism against overfitting if there are too few custom training samples.

test_mode

Is this a test? Just for internal use

Value

Message if the adding has succeeded

Examples

HT29_vcf_file = system.file("extdata/HT29.vcf.gz", package="Uniquorn");
add_custom_vcf_to_database( 
vcf_file_path = HT29_vcf_file,
name_cl = "",
ref_gen = "GRCH37",
safe_mode = FALSE,
test_mode = TRUE )