show_contained_variants_in_library: All variants contained in reference library

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

All variants contained in reference library

Description

This function shows all variants contained in a reference library for a given inclusion weight. Default inclusion weight is 0 (all variants).

Usage

show_contained_variants_in_library(
    ref_gen,
    library_name,
    mutational_weight_inclusion_threshold
)

Arguments

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 CL samples.

Value

Returns a GenomicRanges object that contains the variants

Examples

## Show all variants contained in reference library CELLMINER
show_contained_variants_in_library(
    ref_gen = "GRCH37",
    library_name = "CELLMINER",
    mutational_weight_inclusion_threshold = 0
)

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