SNPhood                 SNPhood: Investigate, quantify and visualise
                        the epigenomic neighbourhood of SNPs using NGS
                        data
SNPhood-class           A class to represent, investigate, quantify and
                        visualise the epigenomic neighbourhood of SNPs
                        using NGS data
SNPhood.o               SNPhood example data
analyzeSNPhood          Main function of _SNPhood_
annotation,SNPhood-method
                        Retrieve the annotation of a 'SNPhood' object.
annotationBins          Get the annotation(names) of the bins in a
                        _SNPhood_ object.
annotationBins2         Get the annotation(names) of bins in a
                        _SNPhood_ object.
annotationDatasets      Get the annotation(names) of the datasets in a
                        _SNPhood_ object.
annotationReadGroups    Get the annotation(names) of the read groups in
                        a _SNPhood_ object.
annotationRegions       Get the annotation of SNP regions for a
                        _SNPhood_ object.
associateGenotypes      Associate genotypes with user regions from a
                        _SNPhood_ object.
changeObjectIntegrityChecking
                        Disable object integrity checking for a
                        _SNPhood_ object.
collectFiles            Helper function to generate a data frame that
                        can be used as input for the function
                        _analyzeSNPhood_
convertToAllelicFractions
                        Convert read counts across read groups to
                        relative fractions from a _SNPhood_ object.
counts,SNPhood-method   Extract count data from a 'SNPhood' object.
deleteDatasets          Delete a particular set of datasets from a
                        _SNPhood_ object.
deleteReadGroups        Delete a particular set of read groups.
deleteRegions           Delete a set of user regions from a _SNPhood_
                        object.
enrichment              Extract enrichment data from an object.
getDefaultParameterList
                        Helper function to generate a default parameter
                        list as input for the function _analyzeSNPhood_
mergeReadGroups         Merges the counts of all read groups for a
                        _SNPhood_ object
nBins                   Get the number of bins for a _SNPhood_ object.
nDatasets               Get the number of datasets for a _SNPhood_
                        object.
nReadGroups             Get the number of read groups for a _SNPhood_
                        object.
nRegions                Get the number of SNP regions for a _SNPhood_
                        object.
parameters              Retrieve the parameters of an object.
plotAllelicBiasResults
                        Graphically summarize the results of the
                        allelic bias analysis for a specific dataset
                        and region.
plotAllelicBiasResultsOverview
                        Visualize the results of the allelic bias
                        analysis across regions or a user-defined
                        genomic range
plotAndCalculateCorrelationDatasets
                        Calculate and plot correlation of region read
                        counts among pairs of input files.
plotAndCalculateWeakAndStrongGenotype
                        Visualizes and calculates strong and weak
                        genotypes.
plotAndClusterMatrix    Clustering of read counts or enrichmens across
                        bins for a specific dataset and read group
plotAndSummarizeAllelicBiasTest
                        Summarize the allelic bias analysis across SNP
                        regions and bins and visualize some of the
                        results.
plotBinCounts           Visualize counts or enrichment for a particular
                        region across bins, datasets, and read groups.
plotClusterAverage      Visualize average enrichment per cluster
plotFDRResults          Graphically summarize the results of the
                        allelic bias analysis for a specific dataset
                        and region.
plotGenotypesPerCluster
                        Visualize average counts/enrichment based on
                        strong and weak genotypes.
plotGenotypesPerSNP     Plot genotype frequencies of regions across
                        datasets.
plotRegionCounts        Visualize the raw read counts across regions or
                        a user-defined genomic range
renameBins              Rename bins.
renameDatasets          Rename datasets.
renameReadGroups        Rename read groups.
renameRegions           Rename regions.
results                 Get results of various analyses performed with
                        a 'SNPhood' object.
testForAllelicBiases    Perform an allelic bias tests for each user
                        region and bin.
