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
1 
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 

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 

Value
score 
Continuous signature scores 
risk 
Binary risk classification, 
Author(s)
Benjamin HaibeKains
References
Loi S, HaibeKains 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 receptorpositive breast cancer treated with tamoxifen", BMC Genomics, 9(1):239
See Also
gene76
Examples
1 2 3 4 5 6 7  ## 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)
