TcgaMutCounts {BiocOncoTK} | R Documentation

## 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

[Package BiocOncoTK version 1.12.1 Index]