decomposeBindingSignal: Decompose binding signal among accepted motifs

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

Description

Gets motif locations and related short reads and select the motifs which are non-skewed: abs(skewness) < 0.3 and more short reads binds closer to site, and show strong binding after decomposition.

Decomposition is performed by using mixtools normalmixEM command fixing mu as motif locations.

Usage

decomposeBindingSignal(
  windowSize,
  replicateNumber,
  acceptedRegionsOutputFile = "BindingRegions",
  acceptedMotifsOutputFile = "BindingMotifsTable",
  currentDir
)

Arguments

windowSize	Window size around binding site. The total region would be 2*windowSize+1
replicateNumber	experiment replicate number
acceptedRegionsOutputFile	File name contains binding regions coordinates and related motifs
acceptedMotifsOutputFile	File name contains motifs coordinates and related information, Pvalue, FE, etc
currentDir	Directory for I/O operations

Value

motifStatistics Ratio of accepted motifs, rejected motifs due to skewnewss, and rejected motifs after decomposition

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