get.bentink.subtypes: Get ovarian cancer subtypes as defined by Bentink et al.,...

In bhklab/consensusOV: Gene expression-based subtype classification for high-grade serous ovarian cancer

Get ovarian cancer subtypes as defined by Bentink et al., 2012

Description

Get ovarian cancer subtypes as defined by Bentink et al., 2012

Usage

get.bentink.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 Bentink.subtypes containing a factor of subtype names; and second value angio containing the ouput of genefu::ovcAngiogenic

References

Bentink et al. Angiogenic mRNA and microRNA gene expression signature predicts a novel subtype of serous ovarian cancer. PloS one (2012).

Examples

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

bhklab/consensusOV documentation built on Feb. 13, 2024, 4:50 a.m.