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

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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

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## 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)

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