get.consensus.subtypes {consensusOV} | R Documentation

## Get consensusOV ovarian cancer subtypes

### Description

Get consensusOV ovarian cancer subtypes

### Usage

    get.consensus.subtypes(expression.matrix, entrez.ids,
      concordant.tumors.only = TRUE, remove.using.cutoff = FALSE,
      percentage.dataset.removed = 0.75,
      .training.dataset = consensus.training.dataset.full,
      .dataset.names.to.keep = names(esets.rescaled.classified.filteredgenes))

### Arguments

`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 `expression.matrix`
`concordant.tumors.only` | Logical. Should the classifier trained only on tumors that are concordantly classified by Helland, Konecny, and Verhaak? Defaults to TRUE.
`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
`.training.dataset` | ExpressionSet containing the training data. Defaults to the pooled dataset across selected MetaGxOvarian datasets.
`.dataset.names.to.keep` | Names of MetaGxOvarian datasets to use for training

### Value

A list with first value `consensusOV.subtypes` containing a factor of subtype names; and second value `rf.probs` containing a matrix of subtype probabilities

### Examples

    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)

[Package consensusOV version 1.6.0 Index]