Man pages for deltaCaptureC
This Package Discovers Meso-scale Chromatin Remodeling from 3C Data

bigBinSizeBig bin size
binnedDeltaPlotPlot of Binned Delta Counts
binnedDeltaSEBinned difference of mean capture-C counts between EScells...
binnedSummarizedExperimentBinned Capture-C counts of EScells and Neurons
binSummarizedExperimentBin a Summarized experiment into a set of bins given by a...
deltaSEDifference of mean capture-C counts between EScells and...
dot-getRunsAndTotalsA helper function for getRunTotals
downshiftDFtoMatrixDownshift from DF to matrix
generatePermutationGenerate permutation for permutation testing
getDeltaSEMake delta summarized experiment:
getLopsidednessGet the lopsidedness statistic
getMeanNormalizedCountsSEMake mean treatment summarized experiment:
getNormalizedCountsSEGet normalized counts
getOverlapWeightsGet the binning factors for one set of GRanges into another
getPValueCutoffThis function returns the significance levels for min, max,...
getRunAndLopsidednessStatisticsGet the distribution of run and lopsidedness statistics
getRunStatisticsThis function is called by getRunsStatisticsDist on the...
getRunStatisticsDistThis takes a list of (scrambled) runs and returns their run...
getRunTotalsGet the runs and their values
getSignificantRegionsGet ths significant regions from delta data
getSizeFactorsDFGet the size factors for count normalization
getSizeFactorsSEGet the size factors for SummarizedExperiment
miniDeltaSEDifference of mean capture-C counts between EScells and...
miniSECapture-C counts of EScells and Neurons
miniSEDFCapture-C counts of EScells and Neurons
numPermutationsNumber of permutations used in example permutation testing.
plotSignificantRegionsThis produces a plot of the region of interest showing...
plotTitleTitle for delta capture-C plot
pValueP-value
rebinToMultipleRebin a SummarizedExperiment to a multiple of its bin width
regionOfInterestRegion of interest surrounding the viewpoint
significanceTypeType for testing significance
significantRegionsRegions of significant remodeling in example data
significantRegionsPlotA plot of the significant regions in the sample data.
smallBinsSmall Bins
smallBinSizeSmall Bin Size
smallerDeltaSEA subset of miniDeltaSE.
smallSetOfSmallBinsSmall Bins
viewpointRegionRegion surrounding the viewpoint
weightsExampleBinsWeights example bins
weightsExampleGrWeights example
deltaCaptureC documentation built on Nov. 8, 2020, 5:31 p.m.