API for wanyuac/GeneMates
Analysing association and physical linkage between bacterial genes
| Global functions | |
|---|---|
| .appendAlleleCounts | Source code |
| .attachDistances | Source code |
| .calcCooccurrenceMatrix | Source code |
| .calcCorCladeProj | Source code |
| .calcDeltaD | Source code |
| .calcDiameters | Source code |
| .calcSummaryStats | Source code |
| .catH0 | Source code |
| .checkAssocOut | Source code |
| .checkDir | Source code |
| .checkFiles | Source code |
| .checkGroupIDs | Source code |
| .checkLmms | Source code |
| .checkQuantileSetting | Source code |
| .clusterLevelSummary | Source code |
| .collapseEdges | Source code |
| .combineCounts | Source code |
| .countCoocurrence | Source code |
| .countCoocurrencePerYear | Source code |
| .countLinkPatterns | Source code |
| .determineSampleDists | Source code |
| .df2matrix | Source code |
| .distsOfEdge | Source code |
| .encodeAlleles | Source code |
| .estimateIBD | Source code |
| .extractLMMoutputs | Source code |
| .findTopClade | Source code |
| .flr | Source code |
| .getAllGenotypes | Source code |
| .getAlleleNames | Source code |
| .getAllelePairs | Source code |
| .getClassName | Source code |
| .getCoStatusPerCluster | Source code |
| .getDistQuantiles | Source code |
| .getDistanceGroups | Source code |
| .getPatterns | Source code |
| .identifyPerfectLinkedCluster | Source code |
| .importTree | Source code |
| .initialiseStageRecords | Source code |
| .linearTrans | Source code |
| .listIddAlleles | Source code |
| .makeEdgeList | Source code |
| .makeFileName | Source code |
| .makeLines | Source code |
| .mergeIdenticalEdges | Source code |
| .mkEdgeSpells | Source code |
| .modifyAssocTable | Source code |
| .pairTestAlleles | Source code |
| .patternToAlleles | Source code |
| .printBtwPatternGenFile | Source code |
| .printIddPatternGenFile | Source code |
| .readFittedLMMs | Source code |
| .readGEMMALogs | Source code |
| .readLine | Source code |
| .recoverHistory | Source code |
| .replaceVals | Source code |
| .restoreAlleleNames | Source code |
| .retrieveEdgeIDs | Source code |
| .retrievePairID | Source code |
| .retriveDistanceMeasurements | Source code |
| .retriveIndex | Source code |
| .runGEMMA | Source code |
| .scoreAssocEvidence | Source code |
| .scoreDistEvidence | Source code |
| .searchForQuery | Source code |
| .searchMinCladePerPair | Source code |
| .setCoreNum | Source code |
| .summariseMinIncCladeOfDists | Source code |
| .summarisePhysDistPerCluster | Source code |
| .testForEffectsPerPattern | Source code |
| .writeData | Source code |
| alleleClusterDistr | Man page Source code |
| allelicCoMatrix | Man page Source code |
| assignPairID | Man page Source code |
| betaSignCongruence | Man page Source code |
| calcAllelicDiveristyPerCountry | Man page Source code |
| calcGeneFreq | Man page Source code |
| compEdgeOccur | Man page Source code |
| comparePvalues | Man page Source code |
| compileGraphs | Man page Source code |
| corCladeProj | Man page Source code |
| corPatternProj | Man page Source code |
| countAlleles | Man page Source code |
| countAllelesPerCountry | Man page Source code |
| countAllelesPerGeneByCountry | Man page Source code |
| countAllelesPerGeneByYear | Man page Source code |
| countAllelesPerYear | Man page Source code |
| countGeneClassLinks | Man page Source code |
| countNeighbours | Man page Source code |
| drawHeatMap | Man page Source code |
| evalPL | Man page Source code |
| extractPairedRows | Man page Source code |
| extractSubgraphs | Man page Source code |
| findMinIncClade | Man page Source code |
| findMinIncCladeOfStrains | Man page Source code |
| findPhysLink | Man page Source code |
| findSeq | Man page Source code |
| getAllelesEarliestAppearance | Man page Source code |
| getAllelesPerPattern | Man page Source code |
| getAssocGenePair | Man page Source code |
| getClusterMemberCooccurrence | Man page Source code |
| getGeneClass | Man page Source code |
| getRowsXY | Man page Source code |
| heatMapPAM | Man page Source code |
| importAllelicPAM | Man page Source code |
| importCoreGenomeSNPs | Man page Source code |
| importGeneticPAM | Man page Source code |
| importPhysicalDists | Man page Source code |
| lmm | Man page Source code |
| mergeIddAlleles | Man page Source code |
| mkCoocurNetwork | Man page Source code |
| mkFilterTSV | Man page Source code |
| mkNetwork | Man page Source code |
| plr | Man page Source code |
| projectSamples | Man page Source code |
| retrieveAlleleSetInfo | Man page Source code |
| ringPlotPAM | Man page Source code |
| screePlotPCs | Man page Source code |
| showGeneContent | Man page Source code |
| summariseCliques | Man page Source code |
| summariseDist | Man page Source code |
| summariseDistsForEdges | Man page Source code |
| summarisePhysDistForClusters | Man page Source code |
| tempNet | Man page Source code |
| testForStruEff | Man page Source code |
| tree2Clades | Man page Source code |
| vertexAttr2Size | Man page Source code |
