AnnotateWithTCGA: Annotate with TCGA

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

Annotate with TCGA

Description

Add TCGA mutation prevalence within a cohort data to the metadata of a genotype object.

Usage

AnnotateWithTCGA(genotype, tcga)

Arguments

genotype	A genotype object
tcga	A data frame that must contain "gene_ensembl_id" and "tcga_percent" columns (character and numeric respectively).

Details

See also ReadTCGA and 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

MyGenotypes <- ReadVcf("MyGenotypes.vcf.gz")
MyTCGA <- ReadTCGA("MyTCGAmutations.tsv")
MyGenotypes <- AnnotateWithTCGA(MyGenotypes,MyTCGA)

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