# RNA Centric Annotation System

## Documentation for package ‘RCAS’ version 1.4.0

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

## 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