API for SNPhood
SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data
| Global functions | |
|---|---|
| .BAMHeaderConsistencyChecks | Source code |
| .calcBinLabelsPlot | Source code |
| .calcBinomTestVector | Source code |
| .calcRandomBackgroundDistr | Source code |
| .calculateGenomeWideBackground | Source code |
| .calculateOverlapsBin | Source code |
| .calculateOverlapsReads | Source code |
| .checkAndConvertDatasetArgument | Source code |
| .checkAndConvertReadGroupArgument | Source code |
| .checkAndConvertRegionArgument | Source code |
| .checkAndCreateIndexFile | Source code |
| .checkConfigFile | Source code |
| .checkObjectValidity | Source code |
| .collectFilesGen | Source code |
| .constructScanBamFlags | Source code |
| .constructScanBamFlagsGen | Source code |
| .createBins | Source code |
| .createSNPhoodObject | Source code |
| .desat | Source code |
| .execInParallelGen | Source code |
| .extractAndNormalize | Source code |
| .extractFromBAM | Source code |
| .extractFromBAMGen | Source code |
| .extractGenotypesVCF | Source code |
| .filterReads | Source code |
| .generateClusterPlot | Source code |
| .generateColorsForReadGroupsAndDatasets | Source code |
| .generateDefaultReadFlags | Source code |
| .getAnnotation | Source code |
| .getBinAxisLabelsForGGPlot | Source code |
| .getBinLabelXAxis | Source code |
| .getBinLabelYAxis | Source code |
| .getCounts | Source code |
| .getEnrichment | Source code |
| .getErrorForOnlyPrepareSamplesCorrelation | Source code |
| .getErrorMessageReadGroupSpecificty | Source code |
| .getFieldsForBAMParsing | Source code |
| .getGenomeData | Source code |
| .getListOfSupportedParameters | Source code |
| .getMemoryProfile | Source code |
| .getParameters | Source code |
| .getSNPGRangesObj | Source code |
| .getThemeForGGPlot | Source code |
| .getUniqueMappabilityData | Source code |
| .getVerticalLineForGGPlot | Source code |
| .getXLab | Source code |
| .getYLab | Source code |
| .identifyGenotypeIncompatibilities | Source code |
| .initBiocParallel | Source code |
| .initSNPhoodObject | Source code |
| .normalizeMatrixForClustering | Source code |
| .onAttach | Source code |
| .pamClustering | Source code |
| .parseAndProcessUserRegions | Source code |
| .parseBed6File | Source code |
| .plotClusterAverage | Source code |
| .plotRegionFeatures | Source code |
| .prettyNum | Source code |
| .printExecutionTime | Source code |
| .produceTitleForPlot | Source code |
| .scaleLibraries | Source code |
| .validSNPhoodObj | Source code |
| SNPhood | Man page |
| SNPhood-class | Man page |
| SNPhood-data | Man page |
| SNPhood-package | Man page |
| SNPhood.o | Man page |
| analyzeSNPhood | Man page Source code |
| annotation | Man page |
| annotation,SNPhood-method | Man page |
| annotationBins | Man page Source code |
| annotationBins2 | Man page Source code |
| annotationDatasets | Man page Source code |
| annotationReadGroups | Man page Source code |
| annotationRegions | Man page Source code |
| associateGenotypes | Man page Source code |
| bins | Man page |
| changeObjectIntegrityChecking | Man page Source code |
| collectFiles | Man page Source code |
| convertToAllelicFractions | Man page Source code |
| counts | Man page |
| counts,SNPhood-method | Man page |
| datasets | Man page |
| deleteDatasets | Man page Source code |
| deleteReadGroups | Man page Source code |
| deleteRegions | Man page Source code |
| enrichment | Man page |
| enrichment,SNPhood-method | Man page |
| getDefaultParameterList | Man page Source code |
| mergeReadGroups | Man page Source code |
| nBins | Man page Source code |
| nDatasets | Man page Source code |
| nReadGroups | Man page Source code |
| nRegions | Man page Source code |
| parameters | Man page |
| parameters,SNPhood-method | Man page |
| plotAllelicBiasResults | Man page Source code |
| plotAllelicBiasResultsOverview | Man page Source code |
| plotAndCalculateCorrelationDatasets | Man page Source code |
| plotAndCalculateWeakAndStrongGenotype | Man page Source code |
| plotAndClusterMatrix | Man page Source code |
| plotAndSummarizeAllelicBiasTest | Man page Source code |
| plotBinCounts | Man page Source code |
| plotClusterAverage | Man page Source code |
| plotFDRResults | Man page Source code |
| plotGenotypesPerCluster | Man page Source code |
| plotGenotypesPerSNP | Man page Source code |
| plotRegionCounts | Man page Source code |
| readGroups | Man page |
| regions | Man page |
| renameBins | Man page Source code |
| renameDatasets | Man page Source code |
| renameReadGroups | Man page Source code |
| renameRegions | Man page Source code |
| results | Man page Source code |
| testForAllelicBiases | Man page Source code |
