Analysis of COMRADES (Cross-Linking Matched RNA and Deep
Sequencing) Data
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Documentation for package ‘comradesOO’ version 0.1.1
Help Pages
| clusterComrades | clusterComrades |
| clusterComrades-method | clusterComrades |
| clusterGrangesList | clusterGrangesList |
| clusterGrangesList-method | clusterGrangesList |
| clusterGrangesList<- | clusterGrangesList<- |
| clusterGrangesList<--method | clusterGrangesList<- |
| clusterNumbers | clusterNumbers |
| clusterNumbers-method | clusterNumbers |
| 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 |
| comradesDataSet | comradesDataSet |
| comradesDataSet-class | comradesDataSet |
| featureInfo | featureInfo |
| featureInfo-method | featureInfo |
| findBasePairsRNAcoFold2 | findBasePairsRNAcoFold2 |
| findBasePairsRNAfold | findBasePairsRNAfold |
| findBasePairsRNAfold2 | findBasePairsRNAfold2 |
| foldComrades | foldComrades |
| foldComrades-method | foldComrades |
| 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 |
| hybFiles | hybFiles |
| hybFiles-method | hybFiles |
| hybToGRanges | hybToGRanges |
| makeExampleComradesDataSet | makeExampleComradesDataSet |
| matrixList | matrixList |
| matrixList-method | matrixList |
| matrixList<- | matrixList |
| matrixList<--method | matrixList |
| plotComparisonArc | plotComparisonArc |
| plotComparisonArc-method | plotComparisonArc |
| plotEnsemblePCA | plotEnsemblePCA |
| plotEnsemblePCA-method | plotEnsemblePCA |
| 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 |
| rnas | rnas |
| rnas-method | rnas |
| rnaSize | rnaSize |
| rnaSize-method | rnaSize |
| sampleChimeras | sampleChimeras |
| sampleNames | sampleNames |
| sampleNames-method | sampleNames |
| sampleTable | sampleTable |
| sampleTable-method | sampleTable |
| subsetHybList2 | subsetHybList2 |
| swapHybs | swapHybs |
| swapHybs2 | swapHybs2 |
| swapHybs3 | swapHybs3 |
| topInteracters | topInteracters |
| topInteracters-method | topInteracters |
| topInteractions | topInteractions |
| topInteractions-method | topInteractions |
| topTranscripts | topTranscripts |
| topTranscripts-method | topTranscripts |
| trimClusters | trimClusters |
| trimClusters-method | trimClusters |