get.subtypes {consensusOV} | R Documentation

## Get ovarian cancer subtypes

### Description

Get ovarian cancer subtypes

### Usage

    get.subtypes(expression.dataset, entrez.ids = NULL,
      method = c("consensusOV", "Helland", "Verhaak", "Konecny", "Bentink"), ...)

### Arguments

`expression.dataset` | Either a matrix of gene expression values with rows as genes, columns as samples; or a BioBase::ExpressionSet object from MetaGxOvarian. If `expression.dataset` is a matrix, then `entrez.ids` must have length equal to the number of rows of `expression.dataset`.
`entrez.ids` | A vector of Entrez Gene IDs, corresponding to the rows of `expression.dataset`
`method` | The subtyping method to use
`...` | Optional parameters to be passed to the low level function

### Value

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

### Examples

    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")

[Package consensusOV version 1.6.0 Index]