Detection of post-transcriptional modifications in high
throughput sequencing data
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Documentation for package ‘RNAmodR’ version 1.19.0
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A B C D E F G H I L M N P R S V misc
-- A --
| aggregate | Aggregate data per positions |
| aggregate-method | Aggregate data per positions |
| aggregateData | Aggregate data per positions |
| aggregateData-method | CoverageSequenceData |
| aggregateData-method | End5SequenceData/End3SequenceData/EndSequenceData |
| aggregateData-method | Functions for ModInosine |
| aggregateData-method | NormEnd5SequenceData/NormEnd3SequenceData |
| aggregateData-method | PileupSequenceData |
| aggregateData-method | ProtectedEndSequenceData |
| aggregateData-method | Aggregate data per positions |
-- B --
| bamfiles | Modifier/ModifierSet functions |
| bamfiles-method | Modifier/ModifierSet functions |
| bamfiles-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
-- C --
| cbind-method | The SequenceData class |
| cbind-method | The SequenceDataFrame class |
| compare | Comparison of Samples |
| compare-method | Comparison of Samples |
| compareByCoord | Comparison of Samples |
| compareByCoord-method | Comparison of Samples |
| conditions-method | Modifier/ModifierSet functions |
| conditions-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
| constructModRanges | RNAmodR developments functions |
| constructModRanges-method | RNAmodR developments functions |
| CoverageSequenceData | CoverageSequenceData |
| CoverageSequenceData-class | CoverageSequenceData |
| CoverageSequenceDataFrame | CoverageSequenceData |
| CoverageSequenceDataFrame-class | CoverageSequenceData |
| csd | Example data in the RNAmodR package |
-- D --
| dataType | Modifier/ModifierSet functions |
| dataType-method | Modifier/ModifierSet functions |
| dataType-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
| DNAModifier-class | The Modifier class |
-- E --
| e3sd | Example data in the RNAmodR package |
| e5sd | Example data in the RNAmodR package |
| End3SequenceData | End5SequenceData/End3SequenceData/EndSequenceData |
| End3SequenceData-class | End5SequenceData/End3SequenceData/EndSequenceData |
| End3SequenceDataFrame | End5SequenceData/End3SequenceData/EndSequenceData |
| End3SequenceDataFrame-class | End5SequenceData/End3SequenceData/EndSequenceData |
| End5SequenceData | End5SequenceData/End3SequenceData/EndSequenceData |
| End5SequenceData-class | End5SequenceData/End3SequenceData/EndSequenceData |
| End5SequenceDataFrame | End5SequenceData/End3SequenceData/EndSequenceData |
| End5SequenceDataFrame-class | End5SequenceData/End3SequenceData/EndSequenceData |
| EndSequenceData | End5SequenceData/End3SequenceData/EndSequenceData |
| EndSequenceData-class | End5SequenceData/End3SequenceData/EndSequenceData |
| EndSequenceDataFrame | End5SequenceData/End3SequenceData/EndSequenceData |
| EndSequenceDataFrame-class | End5SequenceData/End3SequenceData/EndSequenceData |
| esd | Example data in the RNAmodR package |
-- F --
| findMod | Searching for modifications in 'SequenceData' |
| findMod-method | Functions for ModInosine |
| findMod-method | Searching for modifications in 'SequenceData' |
-- G --
| getAggregateData | Aggregate data per positions |
| getAggregateData-method | Aggregate data per positions |
| getData | RNAmodR developments functions |
| getData-method | CoverageSequenceData |
| getData-method | End5SequenceData/End3SequenceData/EndSequenceData |
| getData-method | NormEnd5SequenceData/NormEnd3SequenceData |
| getData-method | PileupSequenceData |
| getData-method | ProtectedEndSequenceData |
| getData-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
| getDataTrack | Visualizing data data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
| getDataTrack-method | CoverageSequenceData |
| getDataTrack-method | End5SequenceData/End3SequenceData/EndSequenceData |
| getDataTrack-method | Functions for ModInosine |
| getDataTrack-method | NormEnd5SequenceData/NormEnd3SequenceData |
| getDataTrack-method | PileupSequenceData |
| getDataTrack-method | ProtectedEndSequenceData |
| getDataTrack-method | Visualizing data data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
-- H --
| hasAggregateData | Aggregate data per positions |
| hasAggregateData-method | Aggregate data per positions |
-- I --
| ICE-Seq | ModInosine |
| Inosine | ModInosine |
-- L --
| labelByCoord | Subsetting data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
| labelByCoord-method | Subsetting data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
-- M --
| mainScore | Modifier/ModifierSet functions |
| mainScore-method | Modifier/ModifierSet functions |
| ModDNASequenceTrack | ModDNASequenceTrack |
| modifications | Searching for modifications in 'SequenceData' |
| modifications-method | Modifier/ModifierSet functions |
| modifications-method | Searching for modifications in 'SequenceData' |
| Modifier | The Modifier class |
| Modifier-class | The Modifier class |
| Modifier-functions | Modifier/ModifierSet functions |
| Modifier-method | The Modifier class |
| ModifierInosine | ModInosine |
| ModifierSet | The ModifierSet class |
| ModifierSet-class | The ModifierSet class |
| ModifierSet-method | The ModifierSet class |
| modifierType | Modifier/ModifierSet functions |
| modifierType-method | Modifier/ModifierSet functions |
| modify | Searching for modifications in 'SequenceData' |
| modify-method | Searching for modifications in 'SequenceData' |
| ModInosine | ModInosine |
| ModInosine-class | ModInosine |
| ModInosine-functions | Functions for ModInosine |
| ModInosine-internals | ModInosine internal functions |
| ModRNASequenceTrack | ModRNASequenceTrack |
| ModSetInosine | ModInosine |
| ModSetInosine-class | ModInosine |
| modType | Modifier/ModifierSet functions |
| modType-method | Modifier/ModifierSet functions |
| msi | Example data in the RNAmodR package |
-- N --
| names-method | Modifier/ModifierSet functions |
| names-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
| ne3sd | Example data in the RNAmodR package |
| ne5sd | Example data in the RNAmodR package |
| NormEnd3SequenceData | NormEnd5SequenceData/NormEnd3SequenceData |
| NormEnd3SequenceData-class | NormEnd5SequenceData/NormEnd3SequenceData |
| NormEnd3SequenceDataFrame | NormEnd5SequenceData/NormEnd3SequenceData |
| NormEnd3SequenceDataFrame-class | NormEnd5SequenceData/NormEnd3SequenceData |
| NormEnd5SequenceData | NormEnd5SequenceData/NormEnd3SequenceData |
| NormEnd5SequenceData-class | NormEnd5SequenceData/NormEnd3SequenceData |
| NormEnd5SequenceDataFrame | NormEnd5SequenceData/NormEnd3SequenceData |
| NormEnd5SequenceDataFrame-class | NormEnd5SequenceData/NormEnd3SequenceData |
| NormEndSequenceData-class | NormEnd5SequenceData/NormEnd3SequenceData |
-- P --
| pesd | Example data in the RNAmodR package |
| PileupSequenceData | PileupSequenceData |
| PileupSequenceData-class | PileupSequenceData |
| PileupSequenceDataFrame | PileupSequenceData |
| PileupSequenceDataFrame-class | PileupSequenceData |
| pileupToCoverage | PileupSequenceData |
| pileupToCoverage-method | PileupSequenceData |
| plotCompare | Comparison of Samples |
| plotCompare-method | Comparison of Samples |
| plotCompareByCoord | Comparison of Samples |
| plotCompareByCoord-method | Comparison of Samples |
| plotData | Visualizing data data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
| plotData-method | Functions for ModInosine |
| plotData-method | Visualizing data data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
| plotDataByCoord | Visualizing data data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
| plotDataByCoord-method | Functions for ModInosine |
| plotDataByCoord-method | Visualizing data data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
| plotROC | ROCR functions for 'Modifier' and 'ModifierSet' objects |
| plotROC-method | ROCR functions for 'Modifier' and 'ModifierSet' objects |
| ProtectedEndSequenceData | ProtectedEndSequenceData |
| ProtectedEndSequenceData-class | ProtectedEndSequenceData |
| ProtectedEndSequenceDataFrame | ProtectedEndSequenceData |
| ProtectedEndSequenceDataFrame-class | ProtectedEndSequenceData |
| psd | Example data in the RNAmodR package |
-- R --
| ranges-method | Modifier/ModifierSet functions |
| ranges-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
| rbind-method | The SequenceData class |
| replicates | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
| replicates-method | Modifier/ModifierSet functions |
| replicates-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
| RNAModifier-class | The Modifier class |
| RNAmodR | RNAmodR |
| RNAmodR-datasets | Example data in the RNAmodR package |
| RNAmodR-development | RNAmodR developments functions |
-- S --
| sdl | Example data in the RNAmodR package |
| sds | Example data in the RNAmodR package |
| seqinfo-method | Modifier/ModifierSet functions |
| seqinfo-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
| seqlevels-method | ModDNASequenceTrack |
| seqlevels-method | ModRNASequenceTrack |
| seqnames-method | ModDNASequenceTrack |
| seqnames-method | ModRNASequenceTrack |
| seqtype-method | Modifier/ModifierSet functions |
| seqtype-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
| seqtype<--method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
| SequenceData | The SequenceData class |
| sequenceData | Modifier/ModifierSet functions |
| SequenceData-class | The SequenceData class |
| SequenceData-functions | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
| SequenceData-method | The SequenceData class |
| sequenceData-method | Modifier/ModifierSet functions |
| SequenceDataFrame | The SequenceDataFrame class |
| SequenceDataFrame-class | The SequenceDataFrame class |
| SequenceDataList | The SequenceDataList class |
| SequenceDataList-class | The SequenceDataList class |
| SequenceDataSet | The SequenceDataSet class |
| SequenceDataSet-class | The SequenceDataSet class |
| SequenceDFrame-class | The SequenceDataFrame class |
| SequenceModDNAStringSetTrack | ModDNASequenceTrack |
| SequenceModDNAStringSetTrack-class | ModDNASequenceTrack |
| SequenceModRNAStringSetTrack | ModRNASequenceTrack |
| SequenceModRNAStringSetTrack-class | ModRNASequenceTrack |
| sequences | Modifier/ModifierSet functions |
| sequences-method | Modifier/ModifierSet functions |
| sequences-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
| settings | Settings for 'Modifier' objects |
| settings-method | Settings for 'Modifier' objects |
| settings<- | Settings for 'Modifier' objects |
| settings<--method | Functions for ModInosine |
| settings<--method | Settings for 'Modifier' objects |
| show-method | Modifier/ModifierSet functions |
| show-method | SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions |
| stats | Retrieving information about used reads in RNAmodR |
| stats-method | Retrieving information about used reads in RNAmodR |
| subset-method | Subsetting data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
| subsetByCoord | Subsetting data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
| subsetByCoord-method | Subsetting data from a 'SequenceData', 'SequenceDataSet', 'SequenceDataList', 'Modifier' or 'ModifierSet' object. |
-- V --
| validAggregate | Modifier/ModifierSet functions |
| validAggregate-method | Modifier/ModifierSet functions |
| validModification | Modifier/ModifierSet functions |
| validModification-method | Modifier/ModifierSet functions |
-- misc --
| .dataTracks-method | ModInosine internal functions |
| [-method | The SequenceDataFrame class |