getAnnotationSynergy {chromVAR} | R Documentation |
getAnnotationSynergy
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)
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 |
should only be run on small number of motifs/kmers/peaksets (very slow!)
synergy matrix
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