Man pages for SNPhood
SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data
| analyzeSNPhood | Main function of _SNPhood_ |
| 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_... |
| annotation-methods | Retrieve the annotation of a 'SNPhood' object. |
| annotationReadGroups | Get the annotation(names) of the read groups in a _SNPhood_... |
| annotationRegions | Get the annotation of SNP regions for a _SNPhood_ object. |
| associateGenotypes | Associate genotypes with user regions from a _SNPhood_... |
| bins-methods | 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... |
| convertToAllelicFractions | Convert read counts across read groups to relative fractions... |
| counts-method | Extract count data from a 'SNPhood' object. |
| datasets-methods | 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-methods | Extract enrichment data from an object. |
| getDefaultParameterList | Helper function to generate a default parameter list as input... |
| mergeReadGroups | Merges the counts of all read groups for a _SNPhood_ object |
| parameters-methods | Retrieve the parameters of an object. |
| plotAllelicBiasResults | Graphically summarize the results of the allelic bias... |
| plotAllelicBiasResultsOverview | Visualize the results of the allelic bias analysis across... |
| plotAndCalculateCorrelationDatasets | Calculate and plot correlation of region read counts among... |
| plotAndCalculateWeakAndStrongGenotype | Visualizes and calculates strong and weak genotypes. |
| plotAndClusterMatrix | Clustering of read counts or enrichmens across bins for a... |
| plotAndSummarizeAllelicBiasTest | Summarize the allelic bias analysis across SNP regions and... |
| plotBinCounts | Visualize counts or enrichment for a particular region across... |
| plotClusterAverage | Visualize average enrichment per cluster |
| plotFDRResults | Graphically summarize the results of the allelic bias... |
| plotGenotypesPerCluster | Visualize average counts/enrichment based on strong and weak... |
| plotGenotypesPerSNP | Plot genotype frequencies of regions across datasets. |
| plotRegionCounts | Visualize the raw read counts across regions or a... |
| readGroups-methods | Get the number of read groups for a _SNPhood_ object. |
| regions-methods | 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'... |
| SNPhood | SNPhood: Investigate, quantify and visualise the epigenomic... |
| SNPhood-class | A class to represent, investigate, quantify and visualise the... |
| SNPhood.o | SNPhood example data |
| testForAllelicBiases | Perform an allelic bias tests for each user region and bin. |
