getPermutedData {chromVAR} | R Documentation

## getPermutedData

### Description

Function to get permuted data while maintaining biases

### Usage

    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

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

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

[Package chromVAR version 1.8.0 Index]