ovcTCGA {genefu} | R Documentation |
This function computes signature scores and risk classifications from gene expression values following the algorithm developed by the TCGA consortium for ovarian cancer.
ovcTCGA(data, annot, gmap = c("entrezgene", "ensembl_gene_id", "hgnc_symbol", "unigene"), do.mapping = FALSE, verbose = FALSE)
data |
Matrix of gene expressions with samples in rows and probes in columns, dimnames being properly defined. |
annot |
Matrix of annotations with one column named as gmap, dimnames being properly defined. |
gmap |
character string containing the |
do.mapping |
|
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
Bell D, Berchuck A, Birrer M et al. (2011) "Integrated genomic analyses of ovarian carcinoma", Nature, 474(7353):609–615
## load the ovcTCGA signature data(sigOvcTCGA) ## load NKI dataset data(nkis) colnames(annot.nkis)[is.element(colnames(annot.nkis), "EntrezGene.ID")] <- "entrezgene" ## compute relapse score ovcTCGA.nkis <- ovcTCGA(data=data.nkis, annot=annot.nkis, gmap="entrezgene", do.mapping=TRUE) table(ovcTCGA.nkis$risk)