computeDeviations: computeDeviations

In GreenleafLab/chromVAR: Chromatin Variation Across Regions

Description

Computes deviations in chromatin accessibility across sets of annotations

Usage

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)

• 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 = SummarizedExperiment,annotations = missingOrNULL: object is SummarizedExperiment, annotations are missing

• 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

• object = MatrixOrmatrix,annotations = missingOrNULL: object is SummarizedExperiment, annotations are missing

Author(s)

Alicia Schep

See Also

computeVariability, plotVariability

Examples

# 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)

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