getPeriodicityTrack {periodicDNA} | R Documentation

## Function to generate a k-mer periodicity track

### Description

This function takes a set of GRanges in a genome, recover the corresponding sequences and divides them using a sliding window. For each sub-sequence, it then computes the PSD value of a k-mer of interest at a chosen period, and generates a linear .bigWig track from these values.

### Usage

    getPeriodicityTrack(
      genome = NULL,
      granges,
      motif = "WW",
      period = 10,
      BPPARAM = setUpBPPARAM(1),
      extension = 1000,
      window_size = 100,
      step_size = 2,
      range_spectrum = seq(5, 50),
      smooth_track = 20,
      bw_file = NULL
    )

### Arguments

`genome` | DNAStringSet, BSgenome or genome ID
`granges` | GRanges object
`motif` | character, k-mer of interest.
`period` | Integer, the period of the k-mer to study (default=10).
`BPPARAM` | split the workload over several processors using BiocParallel
`extension` | Integer, the width the GRanges are going to be extended to (default 1000).
`window_size` | Integer, the width of the bins to split the GRanges objects in (default 100).
`step_size` | Integer, the increment between bins over GRanges (default 2).
`range_spectrum` | Numeric vector, the distances between nucleotides to take into consideration when performing Fast Fourier Transform (default seq_len(50)).
`smooth_track` | Integer, smooth the resulting track
`bw_file` | character, the name of the output bigWig track

### Value

Rlelist and a bigWig track in the working directory.

### Examples

    data(ce11_proms)
    track <- getPeriodicityTrack(
        genome = 'BSgenome.Celegans.UCSC.ce11',
        ce11_proms[1],
        extension = 200,
        window_size = 100,
        step_size = 10,
        smooth_track = 1,
        motif = 'WW',
        period = 10,
        BPPARAM = setUpBPPARAM(1)
    )
    track
    unlink(
        'BSgenome.Celegans.UCSC.ce11_WW_10-bp-periodicity_g-100^10_smooth-1.bw'
    )

[Package periodicDNA version 1.4.0 Index]