getPeriodicity: A function to compute k-mer periodicity in sequence(s).

Description Usage Arguments Value Methods (by class) Examples

View source: R/periodicity.R

Description

This function takes a set of sequences and a k-mer of interest, map a k-mer of interest in these sequences, computes all the pairwise distances (distogram), normalize it for distance decay, and computes the resulting power spectral density of the normalized distogram.

Usage

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getPeriodicity(x, motif, ...)

## S3 method for class 'DNAStringSet'
getPeriodicity(
  x,
  motif,
  range_spectrum = seq(1, 200),
  BPPARAM = setUpBPPARAM(1),
  roll = 3,
  verbose = TRUE,
  sample = 0,
  n_shuffling = 0,
  cores_shuffling = 1,
  cores_computing = 1,
  order = 1,
  ...
)

## S3 method for class 'GRanges'
getPeriodicity(x, motif, genome = "BSgenome.Celegans.UCSC.ce11", ...)

## S3 method for class 'DNAString'
getPeriodicity(x, motif, ...)

Arguments

x

a DNAString, DNAStringSet or GRanges object.

motif

a k-mer of interest

...

Arguments passed to S3 methods

range_spectrum

Numeric vector Range of the distogram to use to run the Fast Fourier Transform on (default: 1:200, i.e. all pairs of k-mers at a maximum of 200 bp from each other).

BPPARAM

split the workload over several processors using BiocParallel

roll

Integer Window to smooth the distribution of pairwise distances (default: 3, to discard the 3-bp periodicity of dinucleotides which can be very strong in vertebrate genomes)

verbose

Boolean

sample

Integer if > 0, will randomly sample this many integers from the dists vector before normalization. This ensures consistency when looking at periodicity in different genomes, since different genomes will have different GC percent

n_shuffling

Integer, how many times should the sequences be shuffled? (default = 0)

cores_shuffling

integer, Number of cores used for shuffling (used if n_shuffling > 0)

cores_computing

integer, split the workload over several processors using BiocParallel (used if n_shuffling > 0)

order

Integer, which order to take into consideration for shuffling (ushuffle python library must be installed for orders > 1) (used if n_shuffling > 0)

genome

genome ID, BSgenome or DNAStringSet object (optional, if x is a GRanges)

Value

A list containing the results of getPeriodicity function.

If getPeriodicity() is ran with n_shuffling > 0, the resulting list also contains PSD values computed when iterating through shuffled sequences.

Methods (by class)

Examples

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data(ce11_proms_seqs)
periodicity_result <- getPeriodicity(
    ce11_proms_seqs[1:100],
    motif = 'TT'
)
head(periodicity_result$PSD)
plotPeriodicityResults(periodicity_result)
#
data(ce11_TSSs)
periodicity_result <- getPeriodicity(
    ce11_TSSs[['Ubiq.']][1:10],
    motif = 'TT',
    genome = 'BSgenome.Celegans.UCSC.ce11'
)
head(periodicity_result$PSD)
plotPeriodicityResults(periodicity_result)
#
data(ce11_TSSs)
periodicity_result <- getPeriodicity(
    ce11_TSSs[['Ubiq.']][1:10],
    motif = 'TT',
    genome = 'BSgenome.Celegans.UCSC.ce11',
    n_shuffling = 10
)
head(periodicity_result$PSD)
plotPeriodicityResults(periodicity_result)

js2264/periodicDNA documentation built on April 22, 2021, 10:43 p.m.