TcgaMutCounts: obtain data frame with counts of mutation per gene symbol for...

In vjcitn/BiocOncoTK: Bioconductor components for general cancer genomics

obtain data frame with counts of mutation per gene symbol for selected tumor type

Description

obtain data frame with counts of mutation per gene symbol for selected tumor type

Usage

TcgaMutCounts(tumor, limit = NULL, db = "isb-cgc:tcga_201607_beta", project)

Arguments

tumor	character(1) defaults to 'BRCA'
limit	numeric(1) defaults to NULL, appended as limit to number of records returned if non-null
db	character(1) BigQuery database name
project	character(1) project code

Value

table as returned by bigrquery::query_exec

Note

This function returns overall mutation count, and many individuals have multiple mutations recorded per gene.

Examples

if (interactive()) {
requireNamespace("bigrquery")
tt = TcgaMutCounts("BRCA", project="cgc-05-0009") # substitute your project name
head(tt)
}  # need authentication

vjcitn/BiocOncoTK documentation built on Feb. 14, 2023, 11:56 p.m.