getAnnotationSynergy

getAnnotationSynergy

getAnnotationSynergy(object, annotations, ...)


  # S4 method for SummarizedExperiment,SummarizedExperiment
getAnnotationSynergy(object,
  annotations, background_peaks = getBackgroundPeaks(object),
  expectation = computeExpectations(object), variabilities = NULL,
  nbg = 25)

# S4 method for SummarizedExperiment,MatrixOrmatrix
getAnnotationSynergy(object,
  annotations, background_peaks = getBackgroundPeaks(object),
  expectation = computeExpectations(object), variabilities = NULL,
  nbg = 25)

# S4 method for SummarizedExperiment,list
getAnnotationSynergy(object, annotations,
  background_peaks = getBackgroundPeaks(object),
  expectation = computeExpectations(object), variabilities = NULL,
  nbg = 25)

# S4 method for MatrixOrmatrix,SummarizedExperiment
getAnnotationSynergy(object,
  annotations, background_peaks, expectation = computeExpectations(object),
  variabilities = NULL, nbg = 25)

# S4 method for MatrixOrmatrix,MatrixOrmatrix
getAnnotationSynergy(object,
  annotations, background_peaks, expectation = computeExpectations(object),
  variabilities = NULL, nbg = 25)

# S4 method for MatrixOrmatrix,list
getAnnotationSynergy(object, annotations,
  background_peaks, expectation = computeExpectations(object),
  variabilities = NULL, nbg = 25)

Arguments

object

result from computeDeviations
annotations

SummarizedExperiment of annotation matches
...

additional arguments
background_peaks

optional, matrix of background peaks
expectation

optional, expected fraction of reads per peak, as computed by computeExpectations
variabilities

optional, variabilities computed from computeVariability
nbg

number of background iterations

Value

synergy matrix

Details

should only be run on small number of motifs/kmers/peaksets (very slow!)

Methods (by class)

  • object = SummarizedExperiment,annotations = SummarizedExperiment: object and annotations are SummarizedExperiment

  • object = SummarizedExperiment,annotations = MatrixOrmatrix: object is SummarizedExperiment, annotations are Matrix

  • object = SummarizedExperiment,annotations = list: object is SummarizedExperiment, annotations are list

  • object = MatrixOrmatrix,annotations = SummarizedExperiment: object and annotations are SummarizedExperiment

  • object = MatrixOrmatrix,annotations = MatrixOrmatrix: object is SummarizedExperiment, annotations are Matrix

  • object = MatrixOrmatrix,annotations = list: object is SummarizedExperiment, annotations are list