show_which_ccls_contain_variant: Cancer cell lines with specific variant

Description Usage Arguments Value Examples

View source: R/Show_database_information.R

Description

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

Usage

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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

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

Uniquorn documentation built on Nov. 8, 2020, 8:07 p.m.