getAnnotationSynergy {chromVAR} | R Documentation

## getAnnotationSynergy

### 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

[Package chromVAR version 1.2.0 Index]