add_custom_vcf_to_database: add_custom_vcf_to_database This function adds the variants of...

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

add_custom_vcf_to_database This function adds the variants of parsed custom CCLs to a monet DB instance

Description

add_custom_vcf_to_database This function adds the variants of parsed custom CCLs to a monet DB instance

Usage

add_custom_vcf_to_database(
    vcf_input_files,
    ref_gen = "GRCH37",
    library_name = "CUSTOM",
    n_threads = 1,
    test_mode = FALSE
)

Arguments

vcf_input_files	a character vector containing the input vcf files. This may be one or many vcf files.
ref_gen	a character string specifying the reference genome version. All training sets are associated with a reference genome version. Default is "GRCH37".
library_name	a character string giving the name of the library to add the cancer cell lines to. Default is "CUSTOM". Library name will be automatically added as a suffix to the identifier.
n_threads	an integer specifying the number of threads to be used.
test_mode	Is this a test? Just for internal use

Value

Message wheather the adding was successful

Examples

HT29_vcf_file = system.file("extdata/HT29_TEST.vcf", package = "Uniquorn");
add_custom_vcf_to_database(
    vcf_input_files = HT29_vcf_file,
    library_name = "CELLMINER",
    ref_gen = "GRCH37",
    n_threads = 1,
    test_mode = TRUE
)

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