computeDeviations

Computes deviations in chromatin accessibility across sets of annotations

computeDeviations(object, annotations, ...)

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

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

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

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

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

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

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

# S4 method for 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

Value

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

Details

multiprocessing using bplapply

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

See also

computeVariability, plotVariability

Examples

# NOT RUN {
# 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)
# }