PWMEmpiricalBackground

PWMEmpiricalBackground-class


  This object contains raw scores for one very long
  sequence, thus it can be very large.


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

PWMEmpiricalBackground function

<dl>
<dt><code>bg.source</code>:</dt><dd>textual description
  of where the background distribution is derived from</dd> <dt><code>bg.fwd</code>:</dt><dd>affinity scores (odds) for the
  forward strand. PWMs as columns</dd> <dt><code>bg.rev</code>:</dt><dd>affinity scores (odds) for the
  reverse strand. PWMs as columns</dd>
 <dt><code>pwms</code>:</dt><dd>the
  pwms for which the background has been compiled</dd>
 </dl> 

Slots

This object contains raw scores for one very long
  sequence, thus it can be very large.

PWMEmpiricalBackground: Background for calculating empirical P-values

Description

Arguments

Slots