getAnnotationSynergy: getAnnotationSynergy

Description Usage Arguments Details Value Methods (by class)

Description

getAnnotationSynergy

Usage

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getAnnotationSynergy(object, annotations, ...)


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

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

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

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

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

## S4 method for signature '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

Details

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

Value

synergy matrix

Methods (by class)


GreenleafLab/chromVAR documentation built on Aug. 20, 2019, 11:39 a.m.