PWMLognBackground

PWMLognBackground-class


  Lognormal background distribution for a set of PWMs


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

PWMLognBackground function

<dl>
<dt><code>bg.source</code>:</dt><dd>textual description
  of where the background distribution is derived from</dd> <dt><code>bg.len</code>:</dt><dd>the length to which the background
  is normalized to. This is a vector of values, can have a
  different value for each motif.</dd> <dt><code>bg.mean</code>:</dt><dd>the mean value of the lognormal
  distribution at bg.len</dd>
 <dt><code>bg.sd</code>:</dt><dd>the standard
  deviation of the lognormal distribution at bg.len</dd> <dt><code>pwms</code>:</dt><dd>the pwms for which the background has
  been compiled</dd>
 </dl> 

Slots

Lognormal background distribution for a set of PWMs

PWMLognBackground: Lognormal background distribution for a set of PWMs

Description

Arguments

Slots