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

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Documentation for package ‘deltaCaptureC’ version 1.22.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

.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