show_which_ccls_contain_variant {Uniquorn} | R Documentation

## 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
    )

[Package Uniquorn version 2.4.0 Index]