getBroadSubtypes {RTCGAToolbox} | R Documentation

## Download expression-based cancer subtypes from the Broad Institute

### Description

Obtain the mRNA expression clustering results from the Broad Institute for a specific cancer code (see getFirehoseDatasets).

### Usage

    getBroadSubtypes(dataset, clust.alg = c("CNMF", "ConsensusPlus"))

### Arguments

`dataset` | A TCGA cancer code, e.g. "OV" for ovarian cancer
`clust.alg` | The selected cluster algorithm, either "CNMF" or "ConsensusPlus" (default "CNMF")

### Value

A `data.frame` of cluster and silhouette values

### Author(s)

Ludwig Geistlinger

### Examples

    co <- getBroadSubtypes("COAD", "CNMF")
    head(co)

[Package RTCGAToolbox version 2.12.1 Index]