# Analysis of RNA Crosslinking Data

## Documentation for package ‘rnaCrosslinkOO’ version 0.1.4

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

## Help Pages

clusterGrangesList | clusterGrangesList
clusterGrangesList-method | clusterGrangesList
clusterGrangesList<- | clusterGrangesList<-
clusterGrangesList<--method | clusterGrangesList<-
clusterNumbers | clusterNumbers
clusterNumbers-method | clusterNumbers
clusterrnaCrosslink | clusterrnaCrosslink
clusterrnaCrosslink-method | clusterrnaCrosslink
clusterTableFolded | clusterTableFolded
clusterTableFolded-method | clusterTableFolded
clusterTableList | clusterTableList
clusterTableList-method | clusterTableList
clusterTableList<- | clusterTableList<-
clusterTableList<--method | clusterTableList<-
compareKnown | compareKnown
compareKnown-method | compareKnown
compareKnownStructures | compareKnownStructures
compareKnownStructures-method | compareKnownStructures
featureInfo | featureInfo
featureInfo-method | featureInfo
findBasePairsRNAcoFold2 | findBasePairsRNAcoFold2
findBasePairsRNAfold | findBasePairsRNAfold
findBasePairsRNAfold2 | findBasePairsRNAfold2
foldrnaCrosslink | foldrnaCrosslink
foldrnaCrosslink-method | foldrnaCrosslink
getAdjacancyMat | getAdjacancyMat
getClusterClusterShortRangeWhole | getClusterClusterShortRangeWhole
getData | getData
getData-method | getData
getInteractions | getInteractions
getInteractions-method | getInteractions
getMatrices | getMatrices
getReverseInteractions | getReverseInteractions
getReverseInteractions-method | getReverseInteractions
group | group
group-method | group
InputFiles | InputFiles
InputFiles-method | InputFiles
InputToGRanges | InputToGRanges
makeExamplernaCrosslinkDataSet | makeExamplernaCrosslinkDataSet
matrixList | matrixList
matrixList-method | matrixList
matrixList<- | matrixList
matrixList<--method | matrixList
plotClusterAgreement | Plot a heatmap that plots the agreements between replicates after clusterrnaCrosslink has been performed
plotClusterAgreement-method | Plot a heatmap that plots the agreements between replicates after clusterrnaCrosslink has been performed
plotClusterAgreementHeat | Plot a heatmap that plots the agreements between replicates after clusterrnaCrosslink has been performed
plotClusterAgreementHeat-method | Plot a heatmap that plots the agreements between replicates after clusterrnaCrosslink has been performed
plotCombinedMatrix | Plots a contact map of two chosen samples for chosen stages in the analysis, with each chosen sample on separate halves of the contact map
plotCombinedMatrix-method | Plots a contact map of two chosen samples for chosen stages in the analysis, with each chosen sample on separate halves of the contact map
plotComparisonArc | plotComparisonArc
plotComparisonArc-method | plotComparisonArc
plotEnsemblePCA | plotEnsemblePCA
plotEnsemblePCA-method | plotEnsemblePCA
plotInteractions | Plots a contact map of interactions of each sample of an RNA (interactor) on the RNA of interest
plotInteractions-method | Plots a contact map of interactions of each sample of an RNA (interactor) on the RNA of interest
plotInteractionsAverage | Plots a contact map of interactions of all samples of an RNA (interactor) on the RNA of interest
plotInteractionsAverage-method | Plots a contact map of interactions of all samples of an RNA (interactor) on the RNA of interest
plotMatrices | Plots a number of contact maps to file of each sample for a stage in the analysis
plotMatrices-method | Plots a number of contact maps to file of each sample for a stage in the analysis
plotMatricesAverage | plotMatricesAverage
plotMatricesAverage-method | plotMatricesAverage
plotStructure | plotStructure
plotStructure-method | plotStructure
printClustersFast | printClustersFast
readNumbers | readNumbers
readNumbers-method | readNumbers
rnaCrosslinkDataSet | rnaCrosslinkDataSet
rnaCrosslinkDataSet-class | rnaCrosslinkDataSet
rnaCrosslinkQC | rnaCrosslinkQC
rnas | rnas
rnas-method | rnas
rnaSize | rnaSize
rnaSize-method | rnaSize
sampleChimeras | sampleChimeras
sampleNames | sampleNames
sampleNames-method | sampleNames
sampleTable | sampleTable
sampleTable-method | sampleTable
subsetInputList2 | subsetInputList2
swapInputs | swapInputs
swapInputs2 | swapInputs2
swapInputs3 | swapInputs3
topInteracters | topInteracters
topInteracters-method | topInteracters
topInteractions | topInteractions
topInteractions-method | topInteractions
topTranscripts | topTranscripts
topTranscripts-method | topTranscripts
trimClusters | trimClusters
trimClusters-method | trimClusters