deviationsCovariability: deviationsCovariability

Description Usage Arguments Details Value Examples

View source: R/kmers.R

Description

deviationsCovariability

Usage

1

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

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# 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,])                         

chromVAR documentation built on Nov. 8, 2020, 6:46 p.m.