deviationsCovariability {chromVAR} | R Documentation

## deviationsCovariability

### Description

deviationsCovariability

### Usage

    deviationsCovariability(object)

### Arguments

`object` | deviations result

### Details

Returns the 'covariability' between motifs/kmers/peaksets. Covariability' is defined as covariance between Z-scores divided by variance of Z-scores for one motif/kmer/peakset (the row).

### Value

'covariability' matrix

### Examples

    # load very small example data
    data(mini_counts, package = "chromVAR")
    motifs <- getJasparMotifs()
    library(motifmatchr)
    motif_ix <- matchMotifs(motifs, mini_counts,
      genome = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19)

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

    # get covariability for just first three motifs
    devcov <- deviationsCovariability(dev[1:3,])

[Package chromVAR version 1.9.0 Index]