R Onto-Tools suite

Documentation for package ‘ROntoTools’ version 1.0.0

alpha1MR	Compute alpha weights
alphaMLG	Compute alpha weights
compute.fischer	Combine independent p-values using the Fischer 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
pe	Pathway-Express: Pathway analysis of signaling pathways
peEdgeRenderInfo	Extract edge render information from a 'pePathway' object
peNodeRenderInfo	Extract node render information from a 'pePathway' object
pePathway	Class that encodes the result of Pathway-Express for a single pathway
pePathway-class	Class that encodes the result of Pathway-Express for a single pathway
peRes	Pathway-Express result class
peRes-class	Pathway-Express result class
plot-method	Plot pathway level statistics
plot-method	Plot Pathway-Express result
plot.pePathway	Plot pathway level statistics
plot.peRes	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.peRes	Summarize the results of a Pathway-Express analysis