purple_cnv_som_gene_process: Process PURPLE CNV Gene File for UMCCRISE

In umccr/gpgr: Genomics Platform Group Reporting

Process PURPLE CNV Gene File for UMCCRISE

Description

Processes the purple.cnv.gene.tsv file. Keeps genes that are in the UMCCR cancer gene list (v24.03.0) and selects columns of interest.

Usage

purple_cnv_som_gene_process(x, g = NULL)

Arguments

x	Path to purple.cnv.gene.tsv file.
g	Path to gene file containing at least three columns: ensembl_gene_symbol: gene name (character). tsgene: is this gene a tumor suppressor (TRUE/FALSE). oncogene: is this gene an oncogene (TRUE/FALSE).

Value

List with two elements:

• tab: Tibble filtered to genes found in g.

• descr: Description of tibble columns.

Examples

x <- system.file("extdata/purple/purple.cnv.gene.tsv", package = "gpgr")
g <- system.file("extdata/ref/somatic_panel-v24.03.0.tsv", package = "gpgr")
(pp <- purple_cnv_som_gene_process(x, g))

umccr/gpgr documentation built on Nov. 28, 2024, 10:16 a.m.