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


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Documentation for package ‘SNPhood’ version 1.6.1

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SNPhood-package SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data
analyzeSNPhood Main function of _SNPhood_
annotation Retrieve the annotation of a 'SNPhood' object.
annotation-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.
bins Get the number of bins for 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 Extract count data from a 'SNPhood' object.
counts-method Extract count data from a 'SNPhood' object.
datasets Get the number of datasets for 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.
enrichment-method 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.
parameters-method 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
readGroups Get the number of read groups for a _SNPhood_ object.
regions Get the number of SNP regions for a _SNPhood_ object.
renameBins Rename bins.
renameDatasets Rename datasets.
renameReadGroups Rename read groups.
renameRegions Rename regions.
results Get results of various analyses performed with a 'SNPhood' object.
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-data SNPhood example data
SNPhood.o SNPhood example data
testForAllelicBiases Perform an allelic bias tests for each user region and bin.