show_contained_variants_for_ccl: Variants In Cancer Cell Line

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

Variants In Cancer Cell Line

Description

This function shows all mutations present in the database for a selected cancer cell line and reference genome.

Usage

show_contained_variants_for_ccl(
    name_ccl, 
    ref_gen,
    library_name,
    mutational_weight_inclusion_threshold
)

Arguments

name_ccl	a character vector giving the identifier of the cancer cell line for which mutations will be shown.
ref_gen	a character vector specifying the reference genome version. All training sets are associated with a reference genome version. Default is "GRCH37".
library_name	Name of the reference library
mutational_weight_inclusion_threshold	Include only mutations with a weight of at least x. Range: 0.0 to 1.0. 1= unique to CL. ~0 = found in many CCL samples.

Value

GenomicRanges object that contains the ccl's variants

Examples

## Show all mutations for Cancer Cell Line 'SK_OV_3'
show_contained_variants_for_ccl(
    name_ccl = "SK_OV_3",
    ref_gen = "GRCH37",
    library_name = "CELLMINER",
    mutational_weight_inclusion_threshold = 0
)

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