purple_cnv_som_gene_process: Process PURPLE CNV Gene File for UMCCRISE

Description Usage Arguments Value Examples

View source: R/purple.R

Description

Processes the purple.cnv.gene.tsv file. Keeps genes that are in the UMCCR cancer gene list and selects columns of interest.

Usage

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Arguments

x

Path to purple.cnv.gene.tsv file.

g

Path to gene file containing at least three columns:

  • symbol: gene name (character).

  • tumorsuppressor: is this gene a tumor suppressor (TRUE/FALSE).

  • oncogene: is this gene an oncogene (TRUE/FALSE).

Value

List with two elements:

Examples

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x <- system.file("extdata/purple/purple.cnv.gene.tsv", package = "gpgr")
g <- system.file("extdata/ref/umccr_cancer_genes_2019-03-20.tsv", package = "gpgr")
(pp <- purple_cnv_som_gene_process(x, g))

umccr/gpgr documentation built on Nov. 25, 2021, 1:15 p.m.