show_which_ccls_contain_variant: Cancer cell lines with specific variant

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

Cancer cell lines with specific variant

Description

This function displays all cancer cell lines in the database which contain a specified variant. Utilizes closed interval coordinates.

Usage

show_which_ccls_contain_variant(
    start,
    end,
    chromosome,
    ref_gen,
    library_name,
    mutational_weight_inclusion_threshold
)

Arguments

start	Start coordinate
end	Stop coordinate
chromosome	Chromosome, 'chr' prefixes are ignored
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

Returns a GenomicRanges object that contains the variant if present. Member ccls can be found in the $Member_ccl vector

Examples

show_which_ccls_contain_variant(
    start = 92030762,
    end = 92030762,
    chromosome = 8,
    ref_gen = "GRCH37",
    library_name = "CELLMINER",
    mutational_weight_inclusion_threshold = 0
)

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