SNPhood {SNPhood} | R Documentation

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

### Description

For more information and an introduction to the package, see the two vignettes.

### Value

Summary analyses and visualizations for the selected genomic regions with respect to, for example, their read counts, genotype, and allelic origin

### `SNPhood` functions

`analyzeSNPhood` `annotation` `annotationBins` `annotationBins2` `annotationDatasets` `annotationReadGroups` `annotationRegions` `associateGenotypes` `collectFiles` `convertToAllelicFractions` `counts` `deleteDatasets` `deleteReadGroups` `deleteRegions` `enrichment` `getDefaultParameterList` `mergeReadGroups` `nBins` `nDatasets` `nReadGroups` `nRegions` `parameters` `plotAllelicBiasResults` `plotAllelicBiasResultsOverview` `plotAndCalculateCorrelationDatasets` `plotAndCalculateWeakAndStrongGenotype` `plotAndClusterMatrix` `plotBinCounts` `plotClusterAverage` `plotGenotypesPerCluster` `plotGenotypesPerSNP` `plotRegionCounts` `renameBins` `renameDatasets` `renameReadGroups` `renameRegions` `results` `testForAllelicBiases`

### Contact Information

We value all the feedback that we receive and will try to reply in a timely manner. Please report any bug that you encounter as well as any feature request that you may have to SNPhood@gmail.com.

[Package SNPhood version 1.16.0 Index]