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

In BiocOncoTK: Bioconductor components for general cancer genomics

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

BiocOncoTK documentation built on Nov. 8, 2020, 6:03 p.m.