R Onto-Tools suite

Documentation for package ‘ROntoTools’ version 2.4.0

alpha1MR	Compute alpha weights
alphaMLG	Compute alpha weights
compute.fisher	Combine independent p-values using the Fisher method
compute.normalInv	Combine independent p-values using the normal inversion method
keggPathwayGraphs	Download and parse KEGG pathway data
keggPathwayNames	Obtain KEGG pathway titles
nodeWeights	Retrieve the node weights of a graph
nodeWeights-method	Retrieve the node weights of a graph
pDis	Primary dis-regulation: Pathway analysis approach based on the unexplained dis-regulation of genes
pDisPathway-class	Class that encodes the result of pDis analysis for a single pathway
pDisRes-class	Primary dis-regulation (pDis) result class
pe	Pathway-Express: Pathway analysis of signaling pathways
peEdgeRenderInfo	Extract edge render information from a 'pePathway-class' object
peNodeRenderInfo	Extract node render information from a 'pePathway-class' object
pePathway-class	Class that encodes the result of Pathway-Express for a single pathway
peRes-class	Pathway-Express result class
plot-method	Plot pathway level statistics
plot-method	Plot Pathway-Express result
setEdgeWeights	Set gene weights based on edge type
setNodeWeights	Set node weights
Summary-method	Summarize the results of a Pathway-Express analysis
Summary-method	Summarize the results of a Pathway-Express analysis
summary.pDisRes	Summarize the results of a primary dis-regulation (pDis) analysis
summary.peRes	Summarize the results of a Pathway-Express analysis