tamr13 {genefu} | R Documentation |
This function computes signature scores from gene expression values following the algorithm used for the Tamoxifen Resistance signature (TAMR13).
tamr13(data, annot, do.mapping = FALSE, mapping, verbose = FALSE)
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 |
|
score |
Continuous signature scores |
risk |
Binary risk classification, |
Benjamin Haibe-Kains
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
## 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)