getPermutedData

Function to get permuted data while maintaining biases

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

Arguments

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

Value

new SummarizedExperiment with addition assays representing permuted version of counts

Details

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

Examples

# NOT RUN {
# Load very small example counts (already filtered)
data(mini_counts, package = "chromVAR")

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

# }