Core function

Core function

# S3 method for GRanges
getPeriodicity(granges, bg = NULL,
  genome = Biostrings::getSeq(BSgenome.Celegans.UCSC.ce11::BSgenome.Celegans.UCSC.ce11),
  ...)

Arguments

granges	a GRanges
bg	a GRanges to estimate background periodicity.
genome	DNAStringSet object. The sequence of an entire genome, obtained for instance by running Biostrings::getSeq(BSgenome.Celegans.UCSC.ce11::BSgenome.Celegans.UCSC.ce11).
...	other parameters forwarded to getPeriodicity.DNAStringSet()

Value

List a list containing the results of getPeriodicity function. The dists vector is the raw vector of all pairwise distances between dinucleotides. The hist dataframe is the distribution of distances over RANGE_FOR_SPECTRUM. The normalized_hist is the raw histogram normalized for decay over increasing distances between pairs of dinucleotides. The spectra object is the output of the FFT applied over normalized_hist. The PSD dataframe contains power spectrum density scores over given frequencies. The signal_to_noise_ratio is a dataframe containing enrichment scores of dinucleotide periodicity, for each period in the period vector. The motif character is the analysed dinucleotide.