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))

    margin(rf.probs)

### 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
`rf.probs` | random forest probabilities for each subtype as returned by `get.consensus.subtypes`

### Value

`get.consensus.subtypes` returns a list with first value `consensusOV.subtypes` containing a factor of subtype labels; and second value `rf.probs` containing a matrix of subtype probabilities.

`margin` returns a numeric vector containing the classification margin scores, i.e. the difference between the top two subtype scores for each tumor.

### Examples

    library(Biobase)
    data(GSE14764.eset)
    expression.matrix <- exprs(GSE14764.eset)
    entrez.ids <- as.character(fData(GSE14764.eset)$EntrezGene.ID)
    sts <- get.consensus.subtypes(expression.matrix, entrez.ids)
    margins <- margin(sts$rf.probs)

[Package consensusOV version 1.14.0 Index]