Package: deltaCaptureC 1.19.0

Michael Shapiro

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

This package discovers meso-scale chromatin remodelling from 3C data. 3C data is local in nature. It givens interaction counts between restriction enzyme digestion fragments and a preferred 'viewpoint' region. By binning this data and using permutation testing, this package can test whether there are statistically significant changes in the interaction counts between the data from two cell types or two treatments.

Authors:Michael Shapiro [aut, cre]

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deltaCaptureC.pdf |deltaCaptureC.html✨
deltaCaptureC/json (API)

# Install 'deltaCaptureC' in R:

install.packages('deltaCaptureC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

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
deltaSE - Difference of mean capture-C counts between EScells and Neurons
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.
pValue - P-value
plotTitle - Title for delta capture-C plot
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.
smallBinSize - Small Bin Size
smallBins - Small Bins
smallSetOfSmallBins - Small Bins
smallerDeltaSE - A subset of miniDeltaSE.
viewpointRegion - Region surrounding the viewpoint
weightsExampleBins - Weights example bins
weightsExampleGr - Weights example

On BioConductor:deltaCaptureC-1.19.0(bioc 3.20)deltaCaptureC-1.18.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

17 exports 0.71 score 67 dependencies

Last updated 2 months agofrom:ecefa7e1f6

Exports:binSummarizedExperiment downshiftDFtoMatrix generatePermutation getDeltaSE getLopsidedness getMeanNormalizedCountsSE getNormalizedCountsSE getOverlapWeights getPValueCutoff getRunAndLopsidednessStatistics getRunStatisticsDist getRunTotals getSignificantRegions getSizeFactorsDF getSizeFactorsSE plotSignificantRegions rebinToMultiple

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel cli codetools colorspace cpp11 crayon curl DelayedArray DESeq2 fansi farver formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle locfit magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig R6 RColorBrewer Rcpp RcppArmadillo rlang S4Arrays S4Vectors scales snow SparseArray SummarizedExperiment sys tibble tictoc UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

Delta Capure-C

Michael Shapiro

Rendered fromdeltaCaptureC.Rmdusingknitr::rmarkdownon Jun 13 2024.

Last update: 2019-09-03
Started: 2019-04-23

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

Package: deltaCaptureC 1.19.0

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

Delta Capure-C

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