endoPredict {genefu} | R Documentation

## Function to compute the endoPredict signature as published by Filipits et al 2011

### Description

This function computes signature scores and risk classifications from gene expression values following the algorithm used for the endoPredict signature as published by Filipits et al 2011.

### Usage

    endoPredict(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

The function works best if data have been noralized with MAS5. 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

ilipits, M., Rudas, M., Jakesz, R., Dubsky, P., Fitzal, F., Singer, C. F., et al. (2011). "A new molecular predictor of distant recurrence in ER-positive, HER2-negative breast cancer adds independent information to conventional clinical risk factors." Clinical Cancer Research, 17(18):6012–6020.

### Examples

    ## load GENE70 signature
    data(sig.endoPredict)
    ## load NKI dataset
    data(vdxs)
    ## compute relapse score
    rs.vdxs <- endoPredict(data=data.vdxs, annot=annot.vdxs, do.mapping=FALSE)

[Package genefu version 2.12.0 Index]