API for mlizhangx/Network-Analysis-for-Repertoire-Sequencing-
Network Analysis of Immune Repertoire
| Global functions | |
|---|---|
| .MUST.doesDataMatchMatrix | Source code |
| .MUST.doesIgraphMatchData | Source code |
| .MUST.doesIgraphMatchMatrix | Source code |
| .MUST.doesLayoutMatchData | Source code |
| .MUST.doesPlotMatchData | Source code |
| .MUST.hasAdjacencyMatrix | Source code |
| .MUST.hasClusterData | Source code |
| .MUST.hasDetails | Source code |
| .MUST.hasElement | Source code |
| .MUST.hasIgraph | Source code |
| .MUST.hasLength | Source code |
| .MUST.hasLength1 | Source code |
| .MUST.hasLength2 | Source code |
| .MUST.hasMultipleRows | Source code |
| .MUST.hasNodeData | Source code |
| .MUST.hasPlots | Source code |
| .MUST.hasPosLength | Source code |
| .MUST.isAdjacencyMatrix | Source code |
| .MUST.isBaseNetworkOutput | Source code |
| .MUST.isChar | Source code |
| .MUST.isCharOrIntegerVector | Source code |
| .MUST.isCharOrLogical | Source code |
| .MUST.isCharOrNumeric | Source code |
| .MUST.isCharOrNumericScalar | Source code |
| .MUST.isCharOrNumericVector | Source code |
| .MUST.isCharOrPosIntegerVector | Source code |
| .MUST.isCharVector | Source code |
| .MUST.isCountColref | Source code |
| .MUST.isDataColref | Source code |
| .MUST.isDataColrefs | Source code |
| .MUST.isDataFrame | Source code |
| .MUST.isDistType | Source code |
| .MUST.isFinite | Source code |
| .MUST.isGgraph | Source code |
| .MUST.isIgraph | Source code |
| .MUST.isInputType | Source code |
| .MUST.isInt | Source code |
| .MUST.isIntegerVector | Source code |
| .MUST.isLayout | Source code |
| .MUST.isLogical | Source code |
| .MUST.isNamedList | Source code |
| .MUST.isNonemptyString | Source code |
| .MUST.isNonneg | Source code |
| .MUST.isNonnegInt | Source code |
| .MUST.isNumeric | Source code |
| .MUST.isNumericScalar | Source code |
| .MUST.isPlotlist | Source code |
| .MUST.isPos | Source code |
| .MUST.isPosInt | Source code |
| .MUST.isPosIntegerVector | Source code |
| .MUST.isSeqColref | Source code |
| .MUST.isSeqColrefs | Source code |
| .MUST.isString | Source code |
| .MUST.isStringOrConnection | Source code |
| .MUST.isStringOrInt | Source code |
| .MUST.isStringOrPosInt | Source code |
| .MUST.isTF | Source code |
| .MUST.isTFOrAuto | Source code |
| .MUST.isValidSeqVector | Source code |
| .RowDropsBySequenceContent | Source code |
| .RowDropsBySequenceLength | Source code |
| .addClusterMembershipWithoutList | Source code |
| .addClusterOnClusterStats | Source code |
| .addColorScheme | Source code |
| .addGeomNodePoint | Source code |
| .calc_clustersnodes_components | Source code |
| .calc_igraph_stats | Source code |
| .calc_seq_stats | Source code |
| .calc_seq_w_max_count | Source code |
| .check | Source code |
| .checkColorNodesBy | Source code |
| .checkColorScheme | Source code |
| .checkColorTitle | Source code |
| .checkCountCol | Source code |
| .checkDataColrefs | Source code |
| .checkDataForColref | Source code |
| .checkDeprecated.buildPublicClusterNetwork | Source code |
| .checkDeprecated.findAssociatedSeqs | Source code |
| .checkDeprecated.findAssociatedSeqs2 | Source code |
| .checkDistType | Source code |
| .checkIDs | Source code |
| .checkMethod | Source code |
| .checkNodeSizeLimits | Source code |
| .checkOutfileLayout | Source code |
| .checkOutputDir | Source code |
| .checkOutputName | Source code |
| .checkOutputType | Source code |
| .checkPlotsAgainstLayout | Source code |
| .checkReadArgs | Source code |
| .checkSizeNodesBy | Source code |
| .checkStatsToInclude | Source code |
| .checkTF | Source code |
| .checkargs.InputFiles | Source code |
| .checkargs.findAssociatedClones | Source code |
| .checkargs.findAssociatedSeqs | Source code |
| .checkargs.findAssociatedSeqs2 | Source code |
| .colorNodesBy.buildPublicClusterNetwork | Source code |
| .colorNodesBy.findPublicClusters | Source code |
| .compileNeighborhood | Source code |
| .computeClusterStats | Source code |
| .convertColRef | Source code |
| .createDirectories | Source code |
| .createOutputDir | Source code |
| .doesDataMatchMatrix | Source code |
| .doesIgraphMatchData | Source code |
| .doesIgraphMatchMatrix | Source code |
| .doesLayoutMatchData | Source code |
| .doesPlotMatchData | Source code |
| .filterByFisherPvalue | Source code |
| .filterClustersBySize | Source code |
| .filterSeqsBySampleMembership | Source code |
| .findAssociatedClonesOneSample | Source code |
| .findPublicClustersOneSample | Source code |
| .generateDualChainNetwork | Source code |
| .generateNetworkGraphFromSeqs | Source code |
| .generateNetworkGraphPlots | Source code |
| .generateSingleChainNetwork | Source code |
| .getClusterFun | Source code |
| .getNbdOneSample | Source code |
| .hamAdjacencyMatSparse | Source code |
| .harmonizePlottingInputs | Source code |
| .hasAdjacencyMatrix | Source code |
| .hasClusterData | Source code |
| .hasDetails | Source code |
| .hasElement | Source code |
| .hasIgraph | Source code |
| .hasLength | Source code |
| .hasLength1 | Source code |
| .hasLength2 | Source code |
| .hasNAs | Source code |
| .hasNodeData | Source code |
| .hasPlots | Source code |
| .hasPosLength | Source code |
| .isAdjacencyMatrix | Source code |
| .isBaseNetworkOutput | Source code |
| .isCharOrIntegerVector | Source code |
| .isCharOrLogical | Source code |
| .isCharOrNumeric | Source code |
| .isCharOrNumericScalar | Source code |
| .isCharOrNumericVector | Source code |
| .isCharOrPosIntegerVector | Source code |
| .isCharVector | Source code |
| .isClusterFun | Source code |
| .isColorNodesBy | Source code |
| .isColorNodesBy1 | Source code |
| .isColorScheme | Source code |
| .isColorScheme1 | Source code |
| .isCountColref | Source code |
| .isDataColref | Source code |
| .isDataColrefs | Source code |
| .isDistType | Source code |
| .isFinite | Source code |
| .isGgraph | Source code |
| .isIgraph | Source code |
| .isInputType | Source code |
| .isInt | Source code |
| .isIntegerVector | Source code |
| .isLayout | Source code |
| .isLogicalVector | Source code |
| .isNamedList | Source code |
| .isNonemptyString | Source code |
| .isNonneg | Source code |
| .isNonnegInt | Source code |
| .isNonnegIntegerVector | Source code |
| .isNumericScalar | Source code |
| .isNumericVector | Source code |
| .isOutputType | Source code |
| .isPlotlist | Source code |
| .isPos | Source code |
| .isPosInt | Source code |
| .isPosIntegerVector | Source code |
| .isSeqColref | Source code |
| .isSeqColrefs | Source code |
| .isStatsToInclude | Source code |
| .isString | Source code |
| .isStringOrConnection | Source code |
| .isStringOrInt | Source code |
| .isStringOrPosInt | Source code |
| .isTF | Source code |
| .isTFOrAuto | Source code |
| .isValidFilename | Source code |
| .isValidFilenamePart | Source code |
| .isValidSeqVector | Source code |
| .levAdjacencyMatSparse | Source code |
| .loadDataFromFile | Source code |
| .loadFile.i | Source code |
| .makePlotSubtitle | Source code |
| .makePlotTitle | Source code |
| .makemsg | Source code |
| .matchDistType | Source code |
| .matchMethod | Source code |
| .noNAs | Source code |
| .onAttach | Source code |
| .onUnload | Source code |
| .orNull | Source code |
| .passColorNodesBy | Source code |
| .patAdjacencyMatSparse | Source code |
| .plotNetworkGraph | Source code |
| .processSubsetCols | Source code |
| .renamePublicNodeStats | Source code |
| .renameSampleLevelNodeStats | Source code |
| .requireOutputDir | Source code |
| .sanitizeFilenamePart | Source code |
| .saveDataGeneric | Source code |
| .saveNetworkObjects | Source code |
| .saveNetworkRDA | Source code |
| .saveNetworkRDS | Source code |
| .savePublicClustersOneSample | Source code |
| .setColorLegendTitle | Source code |
| .setSizeLegendTitle | Source code |
| .sortAdjacencyMatSparse | Source code |
| .stopifnot | Source code |
| .subsetColumns | Source code |
| .subsetDataForAdjacencyMatrix | Source code |
| .updateClusterDetails | Source code |
| .warnifnot | Source code |
| NAIR | Man page |
| NAIR-package | Man page |
| addClusterLabels | Man page Source code |
| addClusterMembership | Man page Source code |
| addClusterStats | Man page Source code |
| addGraphLabels | Man page Source code |
| addNodeNetworkStats | Man page Source code |
| addNodeStats | Man page Source code |
| addPlots | Man page Source code |
| aggregateIdenticalClones | Man page Source code |
| buildAssociatedClusterNetwork | Man page Source code |
| buildNet | Man page |
| buildPublicClusterNetwork | Man page Source code |
| buildPublicClusterNetworkByRepresentative | Man page Source code |
| buildRepSeqNetwork | Man page Source code |
| chooseNodeStats | Man page Source code |
| combineSamples | Man page Source code |
| exclusiveNodeStats | Man page Source code |
| extractLayout | Man page Source code |
| filterInputData | Man page Source code |
| findAssociatedClones | Man page Source code |
| findAssociatedSeqs | Man page Source code |
| findAssociatedSeqs2 | Man page Source code |
| findPublicClusters | Man page Source code |
| generateAdjacencyMatrix | Man page Source code |
| generateNetworkFromAdjacencyMat | Man page Source code |
| generateNetworkGraph | Man page Source code |
| generateNetworkGraphPlots | Man page Source code |
| generateNetworkObjects | Man page Source code |
| getClusterStats | Man page Source code |
| getNeighborhood | Man page Source code |
| hamDistBounded | Man page Source code |
| labelClusters | Man page Source code |
| labelNodes | Man page Source code |
| levDistBounded | Man page Source code |
| loadDataFromFileList | Man page Source code |
| node_stat_settings | Man page Source code |
| plotNetworkGraph | Man page Source code |
| saveNetwork | Man page Source code |
| saveNetworkPlots | Man page Source code |
| simulateToyData | Man page Source code |
| sparseAdjacencyMatFromSeqs | Man page Source code |
