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CoverageSequenceDataFrame() CoverageSequenceData() getData(<CoverageSequenceData>,<BamFileList>,<GRangesList>,<XStringSet>,<ScanBamParam>) aggregateData(<CoverageSequenceData>) getDataTrack(<CoverageSequenceData>)
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CoverageSequenceData |
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End5SequenceDataFrame() End3SequenceDataFrame() EndSequenceDataFrame() End5SequenceData() End3SequenceData() EndSequenceData() getData(<End5SequenceData>,<BamFileList>,<GRangesList>,<XStringSet>,<ScanBamParam>) getData(<End3SequenceData>,<BamFileList>,<GRangesList>,<XStringSet>,<ScanBamParam>) getData(<EndSequenceData>,<BamFileList>,<GRangesList>,<XStringSet>,<ScanBamParam>) aggregateData(<End5SequenceData>) aggregateData(<End3SequenceData>) aggregateData(<EndSequenceData>) getDataTrack(<EndSequenceData>) getDataTrack(<End5SequenceData>) getDataTrack(<End3SequenceData>)
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End5SequenceData/End3SequenceData/EndSequenceData |
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`settings<-`(<ModInosine>) aggregateData(<ModInosine>) findMod(<ModInosine>) getDataTrack(<ModInosine>) plotDataByCoord(<ModInosine>,<GRanges>) plotData(<ModInosine>) plotDataByCoord(<ModSetInosine>,<GRanges>) plotData(<ModSetInosine>)
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Functions for ModInosine |
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ModInosine-internals .dataTracks,ModInosine,GRanges,GRanges,XString-method
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ModInosine internal functions |
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ModInosine() ModSetInosine()
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ModInosine |
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Modifier()
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The Modifier class |
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bamfiles() mainScore() modifierType() modType() dataType() sequenceData() sequences() validAggregate() validModification() show(<Modifier>) conditions(<Modifier>) names(<Modifier>) ranges(<Modifier>) replicates(<Modifier>) seqinfo(<Modifier>) seqtype(<Modifier>) show(<ModifierSet>) conditions(<ModifierSet>) modifications(<ModifierSet>) ranges(<ModifierSet>) replicates(<ModifierSet>) seqinfo(<ModifierSet>) seqtype(<ModifierSet>)
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Modifier/ModifierSet functions |
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ModifierSet()
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The ModifierSet class |
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NormEnd5SequenceDataFrame() NormEnd3SequenceDataFrame() NormEnd5SequenceData() NormEnd3SequenceData() getData(<NormEnd5SequenceData>,<BamFileList>,<GRangesList>,<XStringSet>,<ScanBamParam>) getData(<NormEnd3SequenceData>,<BamFileList>,<GRangesList>,<XStringSet>,<ScanBamParam>) aggregateData(<NormEnd5SequenceData>) aggregateData(<NormEnd3SequenceData>) getDataTrack(<NormEnd5SequenceData>) getDataTrack(<NormEnd3SequenceData>)
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NormEnd5SequenceData/NormEnd3SequenceData |
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PileupSequenceDataFrame() PileupSequenceData() getData(<PileupSequenceData>,<BamFileList>,<GRangesList>,<XStringSet>,<ScanBamParam>) aggregateData(<PileupSequenceData>) getDataTrack(<PileupSequenceData>) pileupToCoverage()
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PileupSequenceData |
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ProtectedEndSequenceDataFrame() ProtectedEndSequenceData() getData(<ProtectedEndSequenceData>,<BamFileList>,<GRangesList>,<XStringSet>,<ScanBamParam>) aggregateData(<ProtectedEndSequenceData>) getDataTrack(<ProtectedEndSequenceData>)
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ProtectedEndSequenceData |
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msi sds sdl psd e5sd e3sd esd csd ne3sd ne5sd pesd
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Example data in the RNAmodR package |
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constructModRanges() getData()
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RNAmodR developments functions |
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RNAmodR
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RNAmodR |
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cbind(<SequenceData>) rbind(<SequenceData>) SequenceData()
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The SequenceData class |
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replicates() show(<SequenceDataFrame>) conditions(<SequenceDataFrame>) bamfiles(<SequenceDataFrame>) dataType(<SequenceDataFrame>) ranges(<SequenceDataFrame>) seqinfo(<SequenceDataFrame>) seqinfo(<SequenceDataFrame>) seqtype(<SequenceDataFrame>) `seqtype<-`(<SequenceDataFrame>) sequences(<SequenceDataFrame>) show(<SequenceData>) getData(<SequenceData>,<BamFileList>,<GRangesList>,<XStringSet>,<ScanBamParam>) bamfiles(<SequenceData>) conditions(<SequenceData>) ranges(<SequenceData>) seqinfo(<SequenceData>) sequences(<SequenceData>) seqtype(<SequenceData>) `seqtype<-`(<SequenceData>) dataType(<SequenceData>) show(<SequenceDataSet>) bamfiles(<SequenceDataSet>) conditions(<SequenceDataSet>) names(<SequenceDataSet>) ranges(<SequenceDataSet>) seqinfo(<SequenceDataSet>) seqtype(<SequenceDataSet>) `seqtype<-`(<SequenceDataSet>) sequences(<SequenceDataSet>) show(<SequenceDataList>) bamfiles(<SequenceDataList>) conditions(<SequenceDataList>) names(<SequenceDataList>) ranges(<SequenceDataList>) seqinfo(<SequenceDataList>) seqtype(<SequenceDataList>) `seqtype<-`(<SequenceDataList>) sequences(<SequenceDataList>)
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SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame
functions |
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cbind(<SequenceDataFrame>) `[`(<SequenceDataFrame>,<ANY>,<ANY>,<ANY>)
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The SequenceDataFrame class |
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SequenceDataList()
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The SequenceDataList class |
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SequenceDataSet()
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The SequenceDataSet class |
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ModDNASequenceTrack() seqnames(<SequenceModDNAStringSetTrack>) seqlevels(<SequenceModDNAStringSetTrack>)
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ModDNASequenceTrack |
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ModRNASequenceTrack() seqnames(<SequenceModRNAStringSetTrack>) seqlevels(<SequenceModRNAStringSetTrack>)
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ModRNASequenceTrack |
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aggregate() aggregateData() getAggregateData() hasAggregateData()
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Aggregate data per positions |
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compare() compareByCoord() plotCompare() plotCompareByCoord()
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Comparison of Samples |
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modifications() modify() findMod()
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Searching for modifications in SequenceData |
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plotData() plotDataByCoord() getDataTrack()
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Visualizing data data from a SequenceData,
SequenceDataSet, SequenceDataList, Modifier or
ModifierSet object. |
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plotROC()
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ROCR functions for Modifier and ModifierSet objects |
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settings() `settings<-`()
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Settings for Modifier objects |
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stats()
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Retrieving information about used reads in RNAmodR |
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subsetByCoord() labelByCoord() subset(<ModifierSet>) subset(<SequenceData>) subset(<SequenceDataSet>) subset(<SequenceDataList>)
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Subsetting data from a SequenceData, SequenceDataSet,
SequenceDataList, Modifier or ModifierSet object. |