getSignificantRegions: Get ths significant regions from delta data

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

Get ths significant regions from delta data

Description

This function takes delta data as a SummarizedExperiment and required ancillary data and returns a GenomicRanges object whose mcols indicate the significant regions.

Usage

getSignificantRegions(
  deltaSE,
  regionOfInterest,
  viewpointRegion,
  smallBinSize,
  bigBinSize,
  numPermutations = 1000,
  pValue = 0.05
)

Arguments

deltaSE	a ranged summarized experiment with a one-column assay giving the delta mean count
regionOfInterest	a GenomicRanges object specifying the region of interest
viewpointRegion	the region withheld from arbitrary permutation
smallBinSize	size to bin original data to for permutation
bigBinSize	size to bin data to for significance testing. Must be a multiple of smallBinSize
numPermutations	= 1000 the number of permutations to be used for permutation testing
pValue	the desired significance level

Value

a GRanges object giving the bigBin binning of region of interest whose mcols gives the values of delta and logicals telling whether the bin is in the viewpoint regsion and whether it rises to statistical significance

michaeldshapiro/deltaCaptureC documentation built on April 21, 2023, 8:18 a.m.