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

Description Usage Arguments Details Value Examples

Function to get permuted data while maintaining biases

1	getPermutedData(object, niterations = 10, w = 0.1, bs = 50)

`object`	SummarizedExperiment
`niterations`	number of background peaks to sample
`w`	parameter controlling similarity of background peaks
`bs`	bin size parameter

Replaces the counts at a given peak with the count from another peak with similar GC content and average accessibility

new SummarizedExperiment with addition assays representing permuted version of counts

# Load very small example counts (already filtered)
data(mini_counts, package = "chromVAR")

# get background peaks
perm_counts <- getPermutedData(mini_counts, niterations = 2)