HotNet: HotNet Class

In funnell/reactomefi: Reactome FI network analysis tools

Description

Represents the results of a HotNet analysis

HotNet constructor

Usage

HotNet(gene.scores, version = c("2009", "2012", "2013"), delta = 1e-04,
  fdr = 0.25, permutations = 100, auto.delta = F)

Arguments

gene.scores	data.frame where the first column contains gene names and the second column contains scores representing the proportion of samples in which the gene is mutated.
version	Version of ReactomeFI network (2009, 2012, 2013).
delta	HotNet delta value
fdr	False discovery rate threshold
permutations	Number of permutations. Largest value is 1000.
auto.delta	If true, algorithm will select a delta value. This option will make the analysis take more time to finish.

Value

HotNet HotNet S4 object containing the results of HotNet analysis. These results should be filtered before using them to generate a network

funnell/reactomefi documentation built on May 16, 2019, 4:05 p.m.