getPeriodicityTrack: Function to generate a k-mer periodicity track

In js2264/periodicDNA: Set of tools to identify periodic occurrences of k-mers in DNA sequences

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'
)

js2264/periodicDNA documentation built on Nov. 3, 2022, 10:47 p.m.