tamr13 {genefu} | R Documentation

## Function to compute the risk scores of the tamoxifen resistance signature (TAMR13)

### Description

This function computes signature scores from gene expression values following the algorithm used for the Tamoxifen Resistance signature (TAMR13).

### Usage

    tamr13(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.
`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.

### Value

A list with items:

- score: Continuous signature scores.

- risk: Binary risk classification, 1 being high risk and 0 being low risk (not implemented, the function will return NA values).

### References

Loi S, Haibe-Kains B, Desmedt C, Wirapati P, Lallemand F, Tutt AM, Gillet C, Ellis P, Ryder K, Reid JF, Daidone MG, Pierotti MA, Berns EMJJ, Jansen MPHM, Foekens JA, Delorenzi M, Bontempi G, Piccart MJ and Sotiriou C (2008) "Predicting prognosis using molecular profiling in estrogen receptor- positive breast cancer treated with tamoxifen", BMC Genomics, 9(1):239

### See Also

gene76

### Examples

    # load TAMR13 signature
    data(sig.tamr13)
    # load VDX dataset
    data(vdxs)
    # compute relapse score
    tamr13.vdxs <- tamr13(data=data.vdxs, annot=annot.vdxs, do.mapping=FALSE)
    summary(tamr13.vdxs$score)

[Package genefu version 2.26.0 Index]