Consensus Pathway Analysis

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Documentation for package ‘RCPA’ version 0.2.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

downloadGEO	Download GEO data
getCePaPathwayCatalogue	Get KEGG pathway catalogue (network) for CePa.ORA and CePa.GSA methods
getCommonDEGenes	Get common significant DE genes from multiple DE Analysis results
getCommonPathways	Retrieve common significant pathways from multiple pathway analysis results
getEntrezAnnotation	Get Entrez annotation
getGeneSets	Get gene sets
getSPIAKEGGNetwork	Get KEGG pathway network for SPIA method
getSupportedPlatforms	Get supported platforms
loadData	Load data from GitHub
plotBarChart	Plot a bar chart of the pathway analysis results
plotDEGeneHeatmap	Plot gene heatmap from a SummarizedExperiment object with DE analysis results
plotForest	Plot pathway forest plot from pathway/geneset/meta analysis results
plotKEGGMap	Plot KEGG map with DE genes
plotMA	Plot MA plot from DE analysis results
plotPathwayHeatmap	Plot pathways heatmap plot from pathway/geneset/meta analysis results
plotPathwayNetwork	Plot a pathway network
plotVennDE	Plot Venn diagram from multiple DE Analysis results
plotVennPathway	Plot Venn diagram from multiple pathway analysis results
plotVolcanoDE	Plot volcano plot from Pathway analysis results
plotVolcanoPathway	Plot volcano plot from Pathway analysis results
processAffymetrix	Process and normalize affymetrix-based dataset
processAgilent	Process and normalize agilent-based dataset
runConsensusAnalysis	Perform Consensus Analysis
runDEAnalysis	Differential expression analysis
runDEMetaAnalysis	Combine DE analysis results
runGeneSetAnalysis	Gene Set Enrichment Analysis
runPathwayAnalysis	Topology-based Pathway Analysis
runPathwayMetaAnalysis	Perform Meta Analysis