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

analyzeSNPhoodMain function of _SNPhood_
annotationBinsGet the annotation(names) of the bins in a _SNPhood_ object.
annotationBins2Get the annotation(names) of bins in a _SNPhood_ object.
annotationDatasetsGet the annotation(names) of the datasets in a _SNPhood_...
annotation-methodsRetrieve the annotation of a 'SNPhood' object.
annotationReadGroupsGet the annotation(names) of the read groups in a _SNPhood_...
annotationRegionsGet the annotation of SNP regions for a _SNPhood_ object.
associateGenotypesAssociate genotypes with user regions from a _SNPhood_...
bins-methodsGet the number of bins for a _SNPhood_ object.
changeObjectIntegrityCheckingDisable object integrity checking for a _SNPhood_ object.
collectFilesHelper function to generate a data frame that can be used as...
convertToAllelicFractionsConvert read counts across read groups to relative fractions...
counts-methodExtract count data from a 'SNPhood' object.
datasets-methodsGet the number of datasets for a _SNPhood_ object.
deleteDatasetsDelete a particular set of datasets from a _SNPhood_ object.
deleteReadGroupsDelete a particular set of read groups.
deleteRegionsDelete a set of user regions from a _SNPhood_ object.
enrichment-methodsExtract enrichment data from an object.
getDefaultParameterListHelper function to generate a default parameter list as input...
mergeReadGroupsMerges the counts of all read groups for a _SNPhood_ object
parameters-methodsRetrieve the parameters of an object.
plotAllelicBiasResultsGraphically summarize the results of the allelic bias...
plotAllelicBiasResultsOverviewVisualize the results of the allelic bias analysis across...
plotAndCalculateCorrelationDatasetsCalculate and plot correlation of region read counts among...
plotAndCalculateWeakAndStrongGenotypeVisualizes and calculates strong and weak genotypes.
plotAndClusterMatrixClustering of read counts or enrichmens across bins for a...
plotAndSummarizeAllelicBiasTestSummarize the allelic bias analysis across SNP regions and...
plotBinCountsVisualize counts or enrichment for a particular region across...
plotClusterAverageVisualize average enrichment per cluster
plotFDRResultsGraphically summarize the results of the allelic bias...
plotGenotypesPerClusterVisualize average counts/enrichment based on strong and weak...
plotGenotypesPerSNPPlot genotype frequencies of regions across datasets.
plotRegionCountsVisualize the raw read counts across regions or a...
readGroups-methodsGet the number of read groups for a _SNPhood_ object.
regions-methodsGet the number of SNP regions for a _SNPhood_ object.
renameBinsRename bins.
renameDatasetsRename datasets.
renameReadGroupsRename read groups.
renameRegionsRename regions.
resultsGet results of various analyses performed with a 'SNPhood'...
SNPhoodSNPhood: Investigate, quantify and visualise the epigenomic...
SNPhood-classA class to represent, investigate, quantify and visualise the...
SNPhood.oSNPhood example data
testForAllelicBiasesPerform an allelic bias tests for each user region and bin.
SNPhood documentation built on May 2, 2018, 3:41 a.m.