oncotypedx {genefu} | R Documentation

## Function to compute the OncotypeDX signature as published by Paik et al. in 2004.

### Description

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.

### Usage

    oncotypedx(data, annot, do.mapping = FALSE, mapping, verbose = FALSE)

### Arguments

`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` | `TRUE` if the mapping through Entrez Gene ids must be performed (in case of ambiguities, the most variant probe is kept for each gene), `FALSE` otherwise. Note that for Affymetrix HGU datasets, the mapping is not necessary.
`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` | `TRUE` to print informative messages, `FALSE` otherwise.

### Details

Note that for Affymetrix HGU datasets, the mapping is not necessary.

### Value

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

### Author(s)

Benjamin Haibe-Kains

### References

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.

### Examples

    ## 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)

[Package genefu version 2.20.0 Index]