getAnnotationCorrelation

getAnnotationCorrelation

getAnnotationCorrelation(object, annotations, ...)


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


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

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


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

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

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

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

Value

correlation 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