getPeriodicityWithIterations {periodicDNA} | R Documentation

## A function to compute PSDs with iterations

### Description

This function computes PSD values of a given k-mer of interest in a set of input sequences. It also iterates the PSD calculation process over shuffled sequences, if n_shuffling is used.

### Usage

    getPeriodicityWithIterations(x, ...)

    ## S3 method for class 'DNAStringSet'
    getPeriodicityWithIterations(
      x,
      motif,
      n_shuffling = 10,
      cores_shuffling = 1,
      cores_computing = 1,
      order = 1,
      verbose = 1,
      ...
    )

    ## S3 method for class 'GRanges'
    getPeriodicityWithIterations(x, genome, ...)

### Arguments

`x` | DNAStringSet, sequences of interest
`...` | Arguments passed to S3 methods
`motif` | character, k-mer of interest
`n_shuffling` | integer, Number of shuffling
`cores_shuffling` | integer, Number of cores used for shuffling
`cores_computing` | integer, split the workload over several processors using BiocParallel
`order` | Integer, which order to take into consideration for shuffling (ushuffle python library must be installed for orders > 1)
`verbose` | integer, Should the function be verbose?
`genome` | genome ID, BSgenome or DNAStringSet object (optional, if x is a GRanges)

### Value

Several metrics

### Methods (by class)

- `DNAStringSet`: S3 method for DNAString

- `GRanges`: S3 method for GRanges

### Examples

    data(ce11_proms_seqs)
    res <- getPeriodicityWithIterations(
        ce11_proms_seqs[1:10],
        genome = 'BSgenome.Celegans.UCSC.ce11',
        motif = 'TT',
        cores_shuffling = 1
    )
    res$observed_PSD
    res$shuffled_PSD

[Package periodicDNA version 1.4.0 Index]