ovcYoshihara {genefu} | R Documentation |
This function computes subtype scores and risk classifications from gene expression values following the algorithm developed by Yoshihara et al, for prognosis in ovarian cancer.
ovcYoshihara(data, annot, hgs, gmap = c("entrezgene", "ensembl_gene_id", "hgnc_symbol", "unigene", "refseq_mrna"), 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. |
hgs |
vector of booleans with TRUE represents the ovarian cancer patients who have a high grade, late stage, serous tumor, FALSE otherwise. This is particularly important for properly rescaling the data. If |
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
Yoshihara K, Tajima A, Yahata T, Kodama S, Fujiwara H, Suzuki M, Onishi Y, Hatae M, Sueyoshi K, Fujiwara H, Kudo, Yoshiki, Kotera K, Masuzaki H, Tashiro H, Katabuchi H, Inoue I, Tanaka K (2010) "Gene expression profile for predicting survival in advanced-stage serous ovarian cancer across two independent datasets", PloS one, 5(3):e9615.
## load the ovcYoshihara signature data(sigOvcYoshihara) ## load NKI dataset data(nkis) colnames(annot.nkis)[is.element(colnames(annot.nkis), "EntrezGene.ID")] <- "entrezgene" ## compute relapse score ovcYoshihara.nkis <- ovcYoshihara(data=data.nkis, annot=annot.nkis, gmap="entrezgene", do.mapping=TRUE) table(ovcYoshihara.nkis$risk)