tamr13: 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

scoreContinuous signature scores
riskBinary 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

Examples

Run this code

## 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)