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 ofambiguities, 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

A list with items: -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.

### References

Filipits, 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 2.26.0 Index]