get.subtypes {consensusOV} | R Documentation |
Get ovarian cancer subtypes
get.subtypes(expression.dataset, entrez.ids = NULL, method = c("consensusOV", "Helland", "Verhaak", "Konecny", "Bentink"), ...)
expression.dataset |
Either a matrix of gene expression values with rows as genes, columns as samples;
or a BioBase::ExpressionSet object from MetaGxOvarian. If |
entrez.ids |
A vector of Entrez Gene IDs, corresponding to the rows of |
method |
The subtyping method to use |
... |
Optional parameters to be passed to the low level function |
A list with first value Konecny.subtypes
containing a factor of subtype names;
and second value spearman.cc.vals
containing the Spearman correlation values per subtype
library(Biobase) data(GSE14764.eset) expression.matrix <- exprs(GSE14764.eset) entrez.ids <- as.character(fData(GSE14764.eset)$EntrezGene.ID) get.subtypes(expression.matrix, entrez.ids, method="Konecny")