gene76 | R Documentation |
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.
gene76(data, er)
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. |
A list with items:
score Continuous signature scores
risk Binary risk classification, 1 being high risk and 0 being low risk.
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.
ggi
# 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)
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