oncotypedx {genefu} | R Documentation |
This function computes signature scores and risk classifications from gene expression values following the algorithm used for the OncotypeDX signature as published by Paik et al. 2004.
oncotypedx(data, annot, do.mapping = FALSE, mapping, verbose = FALSE)
data |
Matrix of gene expressions with samples in rows and probes in columns, dimnames being properly defined. |
annot |
Matrix of annotations with at least one column named "EntrezGene.ID", dimnames being properly defined. |
do.mapping |
|
mapping |
Matrix with columns "EntrezGene.ID" and "probe" used to force the mapping such that the probes are not selected based on their variance. |
verbose |
|
Note that for Affymetrix HGU datasets, the mapping is not necessary.
score |
Continuous signature scores |
risk |
Binary risk classification, |
mapping |
Mapping used if necessary. |
probe |
If mapping is performed, this matrix contains the correspondence between the gene list (aka signature) and gene expression data. |
Benjamin Haibe-Kains
S. Paik, S. Shak, G. Tang, C. Kim, J. Bakker, M. Cronin, F. L. Baehner, M. G. Walker, D. Watson, T. Park, W. Hiller, E. R. Fisher, D. L. Wickerham, J. Bryant, and N. Wolmark (2004) "A Multigene Assay to Predict Recurrence of Tamoxifen-Treated, Node-Negative Breast Cancer", New England Journal of Medicine, 351(27):2817–2826.
## load GENE70 signature data(sig.oncotypedx) ## load NKI dataset data(nkis) ## compute relapse score rs.nkis <- oncotypedx(data=data.nkis, annot=annot.nkis, do.mapping=TRUE) table(rs.nkis$risk)