ggi {genefu} | R Documentation |
This function computes signature scores and risk classifications from gene expression values following the algorithm used for the Gene expression Grade Index (GGI).
ggi(data, annot, do.mapping = FALSE, mapping, hg, 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. |
hg |
Vector containing the histological grade (HG) status of breast cancer patients in the dataset. |
verbose |
|
score |
Continuous signature scores |
risk |
Binary risk classification, |
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. |
Benjamin Haibe-Kains
Sotiriou C, Wirapati P, Loi S, Harris A, Bergh J, Smeds J, Farmer P, Praz V, Haibe-Kains B, Lallemand F, Buyse M, Piccart MJ and Delorenzi M (2006) "Gene expression profiling in breast cancer: Understanding the molecular basis of histologic grade to improve prognosis", Journal of National Cancer Institute, 98:262–272
## load GGI signature data(sig.ggi) ## load NKI dataset data(nkis) ## compute relapse score ggi.nkis <- ggi(data=data.nkis, annot=annot.nkis, do.mapping=TRUE, hg=demo.nkis[ ,"grade"]) table(ggi.nkis$risk)