PWM-class


  A class that represents a Position Weight Matrix (PWM)


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

PWM function

<dl>
<dt><code>id</code>:</dt><dd>a systematic ID given to
  this PWM, could include the source, version, etc</dd> <dt><code>name</code>:</dt><dd>the name of the transcription factor
  (TF) to which the PWM corresponds to</dd> <dt><code>pfm</code>:</dt><dd>Position Frequency Matrix (PFM) from
  which the PWM is derived</dd> <dt><code>prior.params</code>:</dt><dd>Defines prior frequencies of
  the four bases (A,C,G,T), a named vector. These will be
  added to individual values for the PFM and at the same
  time used as background probabilities</dd> <dt><code>pwm</code>:</dt><dd>Final Position Weight Matrix (PWM)
  constructed using prior.params with logarithm base 2</dd>
 </dl> 

Slots

A class that represents a Position Weight Matrix (PWM)

PWM: A class that represents a Position Weight Matrix (PWM)

Description

Arguments

Slots