gene76 {genefu} | R Documentation

## Function to compute the Relapse Score as published by Wang et al. 2005

### Description

This function computes signature scores and risk classifications from gene expression values following the algorithm used for the Relapse Score (GENE76) as published by Wang et al. 2005.

### Usage

    gene76(data, er)

### Arguments

`data` | Matrix of gene expressions with samples in rows and probes in columns, dimnames being properly defined.
`er` | Vector containing the estrogen receptor (ER) status of breast cancer patients in the dataset.

### Value

`score` | Continuous signature scores
`risk` | Binary risk classification, `1` being high risk and `0` being low risk.

### Author(s)

Benjamin Haibe-Kains

### References

Y. Wang and J. G. Klijn and Y. Zhang and A. M. Sieuwerts and M. P. Look and F. Yang and D. Talantov and M. Timmermans and M. E. Meijer-van Gelder and J. Yu and T. Jatkoe and E. M. Berns and D. Atkins and J. A. Foekens (2005) "Gene-Expression Profiles to Predict Distant Metastasis of Lymph-Node-Negative Primary Breast Cancer", Lancet, 365(9460):671–679.

### See Also

`ggi`

### Examples

    ## load GENE76 signature
    data(sig.gene76)
    ## load VDX dataset
    data(vdxs)
    ## compute relapse score
    rs.vdxs <- gene76(data=data.vdxs, er=demo.vdxs[ ,"er"])
    table(rs.vdxs$risk)

[Package genefu version 2.22.1 Index]