# R Onto-Tools suite

## Documentation for package ‘ROntoTools’ version 2.8.0

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

## Help Pages

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