RNA Centric Annotation System


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Documentation for package ‘RCAS’ version 1.8.0

Help Pages

calculateCoverageProfile calculateCoverageProfile
calculateCoverageProfileFromTxdb calculateCoverageProfileFromTxdb
calculateCoverageProfileList calculateCoverageProfileList
calculateCoverageProfileListFromTxdb calculateCoverageProfileListFromTxdb
createControlRegions createControlRegions
createDB createDB
createOrthologousGeneSetList createOrthologousMsigdbDataset
deleteSampleDataFromDB deleteSampleDataFromDB
discoverFeatureSpecificMotifs discoverFeatureSpecificMotifs
extractSequences extractSequences
geneSets Random test gene sets
getFeatureBoundaryCoverage getFeatureBoundaryCoverage
getFeatureBoundaryCoverageBin getFeatureBoundaryCoverageBin
getFeatureBoundaryCoverageMulti getFeatureBoundaryCoverageMulti
getIntervalOverlapMatrix getIntervalOverlapMatrix
getMotifSummaryTable getMotifSummaryTable
getTargetedGenesTable getTargetedGenesTable
getTxdbFeatures getTxdbFeatures
getTxdbFeaturesFromGRanges getTxdbFeaturesFromGRanges
gff Sample GFF file imported as a GRanges object
importBed importBed
importBedFiles importBedFiles
importGtf importGtf
parseMsigdb parseMsigdb
plotFeatureBoundaryCoverage plotFeatureBoundaryCoverage
printMsigdbDataset Print MSIGDB Dataset to a file This function is used to print a MSIGDB dataset into a file. Mostly useful when human data is mapped to another species, and that mapping is required to run the report.
queryGff queryGff
queryRegions Sample BED file imported as a GRanges object
retrieveOrthologs retrieveOrthologs
runGSEA runGSEA
runMotifRG runMotifRG
runReport Generate a RCAS Report for a list of transcriptome-level segments
runReportMetaAnalysis runReportMetaAnalysis
runTopGO runTopGO
summarizeDatabaseContent summarizeDatabaseContent
summarizeQueryRegions summarizeQueryRegions
summarizeQueryRegionsMulti summarizeQueryRegionsMulti