Core function to generate a track of periodicity strenght of a given dinucleotide at a given frequency, over a set of chosen GRanges.

Core function to generate a track of periodicity strenght of a given dinucleotide at a given frequency, over a set of chosen GRanges.

generatePeriodicityTrack(genome = Biostrings::getSeq(BSgenome.Celegans.UCSC.ce11::BSgenome.Celegans.UCSC.ce11),
  granges, MOTIF = "WW", EXTEND.GRANGES = 1000,
  GENOME.WINDOW.SIZE = 100, GENOME.WINDOW.SLIDING = 2,
  BIN.WINDOW.SIZE = 60, BIN.WINDOW.SLIDING = 5,
  RANGE.FOR.SPECTRUM = 1:50, FREQ = 1/10, PROCS = 12,
  bw.file = NULL)

Arguments

genome

DNAStringSet object. Ideally, the sequence of an entire genome, obtained for instance by running Biostrings::getSeq(BSgenome.Celegans.UCSC.ce11::BSgenome.Celegans.UCSC.ce11).
granges

GRanges object (with seqnames overlapping the names of genome).
MOTIF

String Oligonucleotide of interest.
EXTEND.GRANGES

Integer The width the GRanges are going to be extended to (default 1000).
GENOME.WINDOW.SIZE

Integer The width of the bins to split the GRanges objects in (default 100).
GENOME.WINDOW.SLIDING

Integer The increment between bins over GRanges (default 2).
BIN.WINDOW.SIZE

Integer The width of the bins to split each primary bin in (default 60).
BIN.WINDOW.SLIDING

Integer The increment between secondary bins (default 5).
RANGE.FOR.SPECTRUM

Numeric vector The distances between nucleotides to take into consideration when performing Fast Fourier Transform (default 1:50).
FREQ

Float The frequence of the dinucleotide to study (default 1/10).
PROCS

Integer Split the workload over several processors (default 12).
bw.file

String. The name of the output bigWig track

Value

NULL A bigWig track in the working directory.