deriveHeuristicBindingDistribution: build heurisitc distribution around the binding sites

In ManchesterBioinference/Motif2Site: Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions

Description

This function generates heuristic distribution of short reads around binding sites which do not need to deconvolve, total numer of short reads and window size as number of neucleotid around binding sites.

It fits a kernel to the distribution and return the distribution as output. The total sum of returned values is equal to one. It plots this kernel.

Also it calculates FRiPs (Fraction of Reads in Peaks) for each

ChIP-seq and returns it. FRiPs and kernel distributions are measures of goodness of ChIP-seq experiments and selected motifs.

Usage

deriveHeuristicBindingDistribution(
  chipSeq,
  averageBindings,
  windowSize,
  acceptedRegionsOutputFile = "BindingRegions",
  currentDir
)

Arguments

chipSeq	ChIP-seq aligned 1nt short reads
averageBindings	expected short reads number aligned to a random location of genes of given size
windowSize	Window size around binding site. The total region would be 2*windowSize+1
acceptedRegionsOutputFile	Accepted binding regions
currentDir	Directory for I/O operations

Value

FRiPs Fraction of Reads in Peaks

ManchesterBioinference/Motif2Site documentation built on Feb. 13, 2022, 2:03 a.m.