Man pages for deltaCaptureC
This Package Discovers Meso-scale Chromatin Remodeling from 3C Data
| bigBinSize | Big bin size |
| binnedDeltaPlot | Plot of Binned Delta Counts |
| binnedDeltaSE | Binned difference of mean capture-C counts between EScells... |
| binnedSummarizedExperiment | Binned Capture-C counts of EScells and Neurons |
| binSummarizedExperiment | Bin a Summarized experiment into a set of bins given by a... |
| deltaSE | Difference of mean capture-C counts between EScells and... |
| dot-getRunsAndTotals | A helper function for getRunTotals |
| downshiftDFtoMatrix | Downshift from DF to matrix |
| generatePermutation | Generate permutation for permutation testing |
| getDeltaSE | Make delta summarized experiment: |
| getLopsidedness | Get the lopsidedness statistic |
| getMeanNormalizedCountsSE | Make mean treatment summarized experiment: |
| getNormalizedCountsSE | Get normalized counts |
| getOverlapWeights | Get the binning factors for one set of GRanges into another |
| getPValueCutoff | This function returns the significance levels for min, max,... |
| getRunAndLopsidednessStatistics | Get the distribution of run and lopsidedness statistics |
| getRunStatistics | This function is called by getRunsStatisticsDist on the... |
| getRunStatisticsDist | This takes a list of (scrambled) runs and returns their run... |
| getRunTotals | Get the runs and their values |
| getSignificantRegions | Get ths significant regions from delta data |
| getSizeFactorsDF | Get the size factors for count normalization |
| getSizeFactorsSE | Get the size factors for SummarizedExperiment |
| miniDeltaSE | Difference of mean capture-C counts between EScells and... |
| miniSE | Capture-C counts of EScells and Neurons |
| miniSEDF | Capture-C counts of EScells and Neurons |
| numPermutations | Number of permutations used in example permutation testing. |
| plotSignificantRegions | This produces a plot of the region of interest showing... |
| plotTitle | Title for delta capture-C plot |
| pValue | P-value |
| rebinToMultiple | Rebin a SummarizedExperiment to a multiple of its bin width |
| regionOfInterest | Region of interest surrounding the viewpoint |
| significanceType | Type for testing significance |
| significantRegions | Regions of significant remodeling in example data |
| significantRegionsPlot | A plot of the significant regions in the sample data. |
| smallBins | Small Bins |
| smallBinSize | Small Bin Size |
| smallerDeltaSE | A subset of miniDeltaSE. |
| smallSetOfSmallBins | Small Bins |
| viewpointRegion | Region surrounding the viewpoint |
| weightsExampleBins | Weights example bins |
| weightsExampleGr | Weights example |
