get.subtypes: Get ovarian cancer subtypes

Description Usage Arguments Value Examples

View source: R/get.subtypes.R

Description

Get ovarian cancer subtypes

Usage

1
2
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

1
2
3
4
5
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")

bhklab/consensusOV documentation built on Nov. 2, 2018, 1:52 p.m.