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. |