shuffle_motifs {universalmotif} | R Documentation

## Shuffle motifs by column.

### Description

Given a set of motifs, shuffle the columns between them. Currently does not support keeping the 'multifreq' slot. Only the 'bkg', 'nsites', 'strand', and 'bkgsites' slots will be preserved. Uses the same shuffling methods as `shuffle_sequences()`. When shuffling more than one motif, they are shuffled together.

### Usage

    shuffle_motifs(motifs, k = 2, method = "linear", leftovers = "asis")

### Arguments

`motifs` | See `convert_motifs()` for acceptable formats.
`k` | `numeric(1)` K-let size.
`method` | `character(1)` One of `c('linear', 'random')`. Only relevant if `k > 1`. See details.
`leftovers` | `character(1)` For `method = 'random'`. One of `c('asis', 'first', 'split', 'discard')`. See details.

### Details

If `method = 'linear'`, then the input positions are split linearly every `k` columns after which they are shuffled. If `method = random`, then sets of `k`-columns are chosen randonmly before being shuffled. This leaves leftover column islands smaller than `k`; these can be left `asis`, placed `first`, `split` between the beginning and the end, or `discard`ed. See `shuffle_motifs()`.

### Value

Motifs. See `convert_motifs()` for available output formats.

### Author(s)

Benjamin Jean-Marie Tremblay, b2tremblay@uwaterloo.ca

### See Also

`shuffle_sequences()`

[Package universalmotif version 1.0.22 Index]