# R Onto-Tools suite

## Documentation for package ‘ROntoTools’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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