ReadTCGA: Load TCGA data

In nbroguiere/burgertools: Collection of tools extending the functionality of Seurat

Load TCGA data

Description

Read a tsv file with TCGA most commonly mutated genes for a given cohort.

Usage

ReadTCGA(file)

Arguments

file	character(1), the tsv file path.

Details

Read a tab separated value (tsv) file with most commonly mutated genes for a given cancer cohort according to the cancer genome atlas (TCGA). The tsv file should have columns with Simple Somatic Mutation (SSM) Affected Cases in cohort, used to derive a percentage of patients affected, as well as gene (ensembl) IDs. This import function follows the conventions of files exported in tsv from:

https://portal.gdc.cancer.gov/exploration?searchTableTab=genes

Value

A data frame with at least gene_ensembl_id, cases_in_cohort and tcga_percent columns.

Examples

tcga_df <- ReadTCGA("Myfolder/MyTCGAcohortMostCommonMutatedGenes.tsv")

nbroguiere/burgertools documentation built on Jan. 30, 2024, 3:48 a.m.