Analysis of RNA Crosslinking Data
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Documentation for package ‘rnaCrosslinkOO’ version 0.1.4
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 |