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ROntoTools (version 2.0.0)

R Onto-Tools suite

Description

Suite of tools for functional analysis.

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Version

Version

2.0.0

License

CC BY-NC-ND 4.0 + file LICENSE

Maintainer

Calin Voichita

Last Published

February 15th, 2017

Functions in ROntoTools (2.0.0)

subGraphByNodeType

Modified version of the same function from KEGGgraph
peNodeRenderInfo

Extract node render information from a pePathway-class object
pDisPathway-class

Class that encodes the result of pDis analysis for a single pathway
keggPathwayNames

Obtain KEGG pathway titles
peRes-class

Pathway-Express result class
pDis

Primary dis-regulation: Pathway analysis approach based on the unexplained dis-regulation of genes
Summary,peRes-method

Summarize the results of a Pathway-Express analysis
keggPathwayGraphs

Download and parse KEGG pathway data
summary.peRes

Summarize the results of a Pathway-Express analysis
compute.fisher

Combine independent p-values using the Fisher method
pe

Pathway-Express: Pathway analysis of signaling pathways
plot,pePathway,missing-method

Plot pathway level statistics
setNodeWeights

Set node weights
KEGGpathway2Graph

Modified version of the same function from KEGGgraph
alphaMLG

Compute alpha weights
alpha1MR

Compute alpha weights
nodeWeights

Retrieve the node weights of a graph
plot,peRes,missing-method

Plot Pathway-Express result
setEdgeWeights

Set gene weights based on edge type
compute.normalInv

Combine independent p-values using the normal inversion method
pePathway-class

Class that encodes the result of Pathway-Express for a single pathway
pDisRes-class

Primary dis-regulation (pDis) result class
Summary,pDisRes-method

Summarize the results of a Pathway-Express analysis
peEdgeRenderInfo

Extract edge render information from a pePathway-class object
summary.pDisRes

Summarize the results of a primary dis-regulation (pDis) analysis