get.subtypes: Get ovarian cancer subtypes

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

Get ovarian cancer subtypes

Description

Get ovarian cancer subtypes

Usage

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

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 Feb. 13, 2024, 4:50 a.m.