getPeriodicity()is used to compute the power spectral density (PSD) of a chosen k-mer (i.e.
TT) in a set of sequences. The PSD score at a given period indicates the strength of the k-mer at this period.
getPeriodicityTrack()can be used to generate linear tracks representing the periodicity strength of a given k-mer at a chosen period, over genomic loci of interest.
data(ce11_proms) WW_10bp <- getPeriodicityTrack( genome = 'BSgenome.Celegans.UCSC.ce11', granges = ce11_proms, motif = 'WW', period = 10, bw_file = 'WW-10-bp-periodicity_over-proms.bw', BPPARAM = MulticoreParam(12) )
Warning: It is recommended to run this command across many processors using BiocParallel. This command typically takes one day to produce a periodicity track over 15,000 GRanges of 150 bp (with default parameters) using
BPPARAM = MulticoreParam(12). It is highly recommended to run this command in a new