endoPredict: Function to compute the endoPredict signature as published by...

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

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)

bhklab/genefu documentation built on Nov. 30, 2024, 9:03 p.m.