computeDeviations: computeDeviations

Description Usage Arguments Details Value Methods (by class) Author(s) See Also Examples

Description

Computes deviations in chromatin accessibility across sets of annotations

Usage

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computeDeviations(object, annotations, ...)

## S4 method for signature 'SummarizedExperiment,SummarizedExperiment'
computeDeviations(object,
  annotations, background_peaks = getBackgroundPeaks(object),
  expectation = computeExpectations(object))

## S4 method for signature 'SummarizedExperiment,MatrixOrmatrix'
computeDeviations(object,
  annotations, background_peaks = getBackgroundPeaks(object),
  expectation = computeExpectations(object))

## S4 method for signature 'SummarizedExperiment,list'
computeDeviations(object, annotations,
  background_peaks = getBackgroundPeaks(object),
  expectation = computeExpectations(object))

## S4 method for signature 'SummarizedExperiment,missingOrNULL'
computeDeviations(object,
  annotations, background_peaks = getBackgroundPeaks(object),
  expectation = computeExpectations(object))

## S4 method for signature 'MatrixOrmatrix,SummarizedExperiment'
computeDeviations(object,
  annotations, background_peaks, expectation = computeExpectations(object))

## S4 method for signature 'MatrixOrmatrix,MatrixOrmatrix'
computeDeviations(object, annotations,
  background_peaks, expectation = computeExpectations(object))

## S4 method for signature 'MatrixOrmatrix,list'
computeDeviations(object, annotations,
  background_peaks, expectation = computeExpectations(object))

## S4 method for signature 'MatrixOrmatrix,missingOrNULL'
computeDeviations(object, annotations,
  background_peaks, expectation = computeExpectations(object))

Arguments

object

chromVARCounts object

annotations

chromVARAnnotations object

...

additional arguments

background_peaks

(optional) background peaks matrix computed using getBackgroundPeaks, computed internally with default paramaters if not provided

expectation

(optional) expectations computed using computeExpectations, computed automatically if not provided

Details

multiprocessing using bplapply

Value

chromVARDeviations-class, which inherits from SummarizedExperiment, and has two assays: deviations and deviation scores.

Methods (by class)

Author(s)

Alicia Schep

See Also

computeVariability, plotVariability

Examples

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# Register BiocParallel
BiocParallel::register(BiocParallel::SerialParam())
# Load very small example counts (already filtered)
data(mini_counts, package = "chromVAR")
# load annotation matrix; result from matchMotifs
data(mini_ix, package = "chromVAR")

# computing deviations
dev <- computeDeviations(object = mini_counts,
                         annotations = mini_ix)

chromVAR documentation built on Nov. 8, 2020, 6:46 p.m.