This Package Discovers Meso-scale Chromatin Remodeling from 3C Data


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Documentation for package ‘deltaCaptureC’ version 1.22.0

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.getRunsAndTotals A helper function for getRunTotals
bigBinSize Big bin size
binnedDeltaPlot Plot of Binned Delta Counts
binnedDeltaSE Binned difference of mean capture-C counts between EScells and Neurons
binnedSummarizedExperiment Binned Capture-C counts of EScells and Neurons
binSummarizedExperiment Bin a Summarized experiment into a set of bins given by a GRanges object
deltaSE Difference of mean capture-C counts between EScells and Neurons
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, "abs" and lopsidedness.
getRunAndLopsidednessStatistics Get the distribution of run and lopsidedness statistics
getRunStatistics This function is called by getRunsStatisticsDist on the individual elements of a list of scrambled runs.
getRunStatisticsDist This takes a list of (scrambled) runs and returns their run statistics
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 Neurons
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 regions of significance.
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