API for SNPhood
SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data

Global functions
BAMHeaderConsistencyChecks 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
calcBinLabelsPlot Source code
calcBinomTestVector Source code
calcRandomBackgroundDistr Source code
calculateGenomeWideBackground Source code
calculateOverlapsBin Source code
calculateOverlapsReads Source code
changeObjectIntegrityChecking Man page Source code
checkAndConvertDatasetArgument Source code
checkAndConvertReadGroupArgument Source code
checkAndConvertRegionArgument Source code
checkAndCreateIndexFile Source code
checkConfigFile Source code
checkObjectValidity Source code
collectFiles Man page Source code
collectFilesGen Source code
constructScanBamFlags Source code
constructScanBamFlagsGen Source code
convertToAllelicFractions Man page Source code
counts Man page
counts,SNPhood-method Man page
createBins Source code
createSNPhoodObject Source code
datasets Man page
deleteDatasets Man page Source code
deleteReadGroups Man page Source code
deleteRegions Man page Source code
dentifyGenotypeIncompatibilities Source code
desat Source code
determineHeterozygosity Source code
enrichment Man page
enrichment,SNPhood-method Man page
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
getDefaultParameterList Man page 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
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
nitBiocParallel Source code
nitSNPhoodObject Source code
normalizeMatrixForClustering Source code
onAttach Source code
pamClustering Source code
parameters Man page
parameters,SNPhood-method Man page
parseAndProcessUserRegions Source code
parseBed6File Source code
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 Source code
plotFDRResults Man page Source code
plotGenotypesPerCluster Man page Source code
plotGenotypesPerSNP Man page Source code
plotRegionCounts Man page Source code
plotRegionFeatures Source code
prettyNum Source code
printExecutionTime Source code
produceTitleForPlot 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
scaleLibraries Source code
testForAllelicBiases Man page Source code
validSNPhoodObj Source code
SNPhood documentation built on Nov. 1, 2018, 2:21 a.m.