genefu (version 2.4.2)

gene76: 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.

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)