oncotypedx: Function to compute the OncotypeDX signature as published by...

In bhklab/genefu: Computation of Gene Expression-Based Signatures in Breast Cancer

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, do.scaling=TRUE,
  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.
do.scaling	Should the data be scaled?
verbose	TRUE to print informative messages, FALSE otherwise.

Details

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

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)

bhklab/genefu documentation built on June 2, 2022, 2:56 p.m.