computeDeviations {chromVAR} | R Documentation |
Computes deviations in chromatin accessibility across sets of annotations
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))
object |
chromVARCounts object |
annotations |
chromVARAnnotations object |
... |
additional arguments |
background_peaks |
(optional) background peaks matrix computed using
|
expectation |
(optional) expectations computed using
|
multiprocessing using bplapply
chromVARDeviations-class
, which inherits from
SummarizedExperiment, and has two assays: deviations and deviation scores.
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
Alicia Schep
computeVariability
, plotVariability
# 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)