Ensemble of Gene Set Enrichment Analyses

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Documentation for package ‘EGSEA’ version 1.2.0

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EGSEA-package Ensemble of Gene Enrichment Analysis (EGSEA)
$-method The EGSEAResults class
$-method The GSCollectionIndex class
buildCustomIdx Custom Gene Set Collection Index
buildGeneSetDBIdx Gene Set Collection Indexes from the GeneSetDB Database
buildIdx Generate Gene Set Collection Indexes from the MSigDB and KEGG Databases
buildKEGGIdx Gene Set Collection Index from the KEGG Database
buildMSigDBIdx Gene Set Collection Indexes from the MSigDB Database
EGSEA Ensemble of Gene Enrichment Analysis (EGSEA)
egsea Ensemble of Gene Set Enrichment Analyses Function
egsea.base EGSEA Base GSE Methods
egsea.cnt Ensemble of Gene Set Enrichment Analyses Function
egsea.combine EGSEA P-value Combining Options
egsea.ora Over-representation Analysis with EGSEA Reporting Capabilities
egsea.sort EGSEA Result Sorting Options
EGSEAResults The EGSEAResults class
EGSEAResults-class The EGSEAResults class
getlimmaResults The EGSEAResults class
getlimmaResults-method The EGSEAResults class
getSetByID The GSCollectionIndex class
getSetByID-method The GSCollectionIndex class
getSetByName The GSCollectionIndex class
getSetByName-method The GSCollectionIndex class
getSetScores The EGSEAResults class
getSetScores-method The EGSEAResults class
GSCollectionIndex The GSCollectionIndex class
GSCollectionIndex-class The GSCollectionIndex class
limmaTopTable The EGSEAResults class
limmaTopTable-method The EGSEAResults class
plotGOGraph The EGSEAResults class
plotGOGraph-method The EGSEAResults class
plotHeatmap The EGSEAResults class
plotHeatmap-method The EGSEAResults class
plotMethods The EGSEAResults class
plotMethods-method The EGSEAResults class
plotPathway The EGSEAResults class
plotPathway-method The EGSEAResults class
plotSummary The EGSEAResults class
plotSummary-method The EGSEAResults class
plotSummaryHeatmap The EGSEAResults class
plotSummaryHeatmap-method The EGSEAResults class
show-method The EGSEAResults class
show-method The GSCollectionIndex class
showSetByID The EGSEAResults class
showSetByID-method The EGSEAResults class
showSetByName The EGSEAResults class
showSetByName-method The EGSEAResults class
summary-method The EGSEAResults class
summary-method The GSCollectionIndex class
topSets The EGSEAResults class
topSets-method The EGSEAResults class