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

## Documentation for package ‘SNPhood’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.