getAnnotationSynergy: getAnnotationSynergy

In GreenleafLab/chromVAR: Chromatin Variation Across Regions

Description

getAnnotationSynergy

Usage

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)

• 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

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