get.consensus.subtypes {consensusOV} | R Documentation |
Get consensusOV ovarian cancer subtypes
get.consensus.subtypes(expression.matrix, entrez.ids, .dataset.names.to.keep = names(esets.rescaled.classified.filteredgenes), remove.using.cutoff = FALSE, percentage.dataset.removed = 0.75)
expression.matrix |
A matrix of gene expression values with rows as genes, columns as samples. |
entrez.ids |
A vector of Entrez Gene IDs, corresponding to the rows of |
.dataset.names.to.keep |
Names of MetaGxOvarian datasets to use for training |
remove.using.cutoff |
Specify whether to classify NA for samples that do not meet a margin cutoff |
percentage.dataset.removed |
If remove.using.cutoff is TRUE, then classify this percentage of samples to NA based on margin values |
A list with first value consensusOV.subtypes
containing a factor of subtype names;
and second value rf.probs
containing a matrix of subtype probabilities
library(Biobase) data(GSE14764.eset) expression.matrix <- exprs(GSE14764.eset) entrez.ids <- as.character(fData(GSE14764.eset)$EntrezGene.ID) get.consensus.subtypes(expression.matrix, entrez.ids)