getPermutedData {chromVAR} | R Documentation |
Function to get permuted data while maintaining biases
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)