getPermutedData: getPermutedData

Description Usage Arguments Details Value Examples

View source: R/background_peaks.R

Description

Function to get permuted data while maintaining biases

Usage

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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

Details

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

Value

new SummarizedExperiment with addition assays representing permuted version of counts

Examples

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

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

GreenleafLab/chromVAR documentation built on Aug. 20, 2019, 11:39 a.m.