scmgene.robust {genefu} | R Documentation

## Subtype Clustering Model using only ESR1, ERBB2 and AURKA genes for identification of breast cancer molecular subtypes

### Description

List of parameters defining the Subtype Clustering Model as published in Wirapati et al 2009 and Desmedt et al 2008 but using single genes instead of gene modules.

### Usage

    data(scmgene.robust)

### Format

List of parameters for SCMGENE:

`parameters`

  List of parameters for the mixture of three Gaussians (ER-/HER2-, HER2+ and ER+/HER2-) that define the Subtype Clustering Model. The structure is the same than for an `Mclust` object.

`cutoff.AURKA`

  Cutoff for AURKA module score in order to identify ER+/HER2- High Proliferation (aka Luminal B) tumors and ER+/HER2- Low Proliferation (aka Luminal A) tumors.

`mod`

  ESR1, ERBB2 and AURKA modules.

### Source

http://clincancerres.aacrjournals.org/content/14/16/5158.abstract?ck=nck

### References

Desmedt C, Haibe-Kains B, Wirapati P, Buyse M, Larsimont D, Bontempi G, Delorenzi M, Piccart M, and Sotiriou C (2008) "Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes", Clinical Cancer Research, 14(16):5158–5165.

### Examples

    data(scmgene.robust)
    str(scmgene.robust, max.level=1)

[Package genefu version 2.20.0 Index]