getPeriodicity.DNAStringSet.Rd# S3 method for DNAStringSet getPeriodicity(seqs, bg_seqs = NULL, model_background = FALSE, motif = "WW", RANGE_FOR_SPECTRUM = 1:200, period = seq(2, 20, 1), plot = FALSE, cores = 2, roll = 3, verbose = TRUE, sample = 0, doZscore = TRUE)
| seqs | a DNAStringSet |
|---|---|
| bg_seqs | a DNAStringSet (ideally from random loci) for genome background model |
| model_background | Boolean Should the genome background be taken into account during normalization? |
| motif | a dinucleotide of interest |
| RANGE_FOR_SPECTRUM | Numeric vector The distances between nucleotides to take into consideration when performing Fast Fourier Transform. |
| period | Vector a numerical vector of periods to extract. |
| plot | Boolean Should the FFT results be plotted? |
| cores | Integer How many processors should be used to parallelize the mapping? |
| 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 |