motifEcdf

a set of motifs, either a list of frequency
  matrices, or a list of PWM objects. If frequency matrices
  are given, the background distribution is fitted from
  bg.seq.

motifs

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

organism

a set of background sequence (either this
  or organism needs to be specified!). Can be a DNAString
  or DNAStringSet object.

bg.seq

if to do the fitting only on a small subset
  of the data (only in combination with <code>organism</code>).
  Useful only for code testing!

quick

the pseudo count which is shared
  between nucleotides when frequency matrices are given

pseudo.count


  Calculate the empirical distribution score distribution
  for a set of motifs


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.

motifEcdf: Calculate the empirical distribution score distribution for a set of motifs

Description

Usage

Arguments

Value