getBackgroundFrequencies

either a name of the organisms for which
  the background should be compiled (supported names are "dm3", 
  "mm9" and "hg19"),
  a <code>BSgenome</code> object, <code>DNAStringSet</code>, or list of <code>DNAString</code> objects

organism

the number to which the frequencies
  sum up to, by default 1

pseudo.count

if to preform fitting on a reduced set of
  100 promoters. This will not give as good results but is
  much quicker than fitting to all the promoters (~10k).
  Usage of this parameter is recommended only for testing
  and rough estimates.

quick


  Estimate the background frequencies of A,C,G,T on a set
  of promoters from an organism


A toolkit of high-level functions for DNA motif scanning
and enrichment analysis built upon Biostrings. The main
functionality is PWM enrichment analysis of already known PWMs
(e.g. from databases such as MotifDb), but the package also
implements high-level functions for PWM scanning and
visualisation. The package does not perform "de novo" motif
discovery, but is instead focused on using motifs that are
either experimentally derived or computationally constructed by
other tools.

Robert Stojnic

PWMEnrich

PWM enrichment analysis

getBackgroundFrequencies function

Estimate the background frequencies of A,C,G,T on a set
  of promoters from an organism

getBackgroundFrequencies: Get the four nucleotides background frequencies

Description

Usage

Arguments

Examples