R Onto-Tools suite


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Documentation for package ‘ROntoTools’ version 1.0.0

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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