deviationsCovariability: deviationsCovariability
In GreenleafLab/chromVAR: Chromatin Variation Across Regions

Description Usage Arguments Details Value Examples

deviationsCovariability

1	deviationsCovariability(object)

object

deviations result

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).

'covariability' matrix

# 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,])