get.verhaak.subtypes {consensusOV}R Documentation

Get ovarian cancer subtypes as defined by Verhaak et al., 2013

Description

Get ovarian cancer subtypes as defined by Verhaak et al., 2013

Usage

get.verhaak.subtypes(expression.matrix, entrez.ids)

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

Value

A list with first value Verhaak.subtypes containing a factor of subtype names; and second value gsva containing the GSVA subtype scores

References

Verhaak et al. Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. The Journal of Clinical Investigation (2013)

Examples

library(Biobase)
data(GSE14764.eset)
expression.matrix <- exprs(GSE14764.eset)
entrez.ids <- as.character(fData(GSE14764.eset)$EntrezGene.ID)
get.konecny.subtypes(expression.matrix, entrez.ids)

[Package consensusOV version 1.10.0 Index]