# Detection of post-transcriptional modifications in high throughput sequencing data

## Documentation for package ‘RNAmodR’ version 1.6.0

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

## Help Pages

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