PWMGEVBackground

PWMGEVBackground-class


  The three parameters of the GEV distribution are fitted
  by doing linear regression on log of sequence length.


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

PWMGEVBackground function

<dl>
<dt><code>bg.source</code>:</dt><dd>textual description
  of where the background distribution is derived from</dd> <dt><code>bg.loc</code>:</dt><dd>linear regression model for
  estimating the location parameter based on log(L), list
  of lm objects of PWMs</dd>
 <dt><code>bg.scale</code>:</dt><dd>linear
  regression model for estimating the scale parameter based
  on log(L), list of lm objects of PWMs</dd> <dt><code>bg.shape</code>:</dt><dd>linear regression model for
  estimating the shape parameter based on log(L), list of
  lm objects of PWMs</dd>
 <dt><code>pwms</code>:</dt><dd>the pwms for
  which the background has been compiled</dd>
 </dl> 

Slots

The three parameters of the GEV distribution are fitted
  by doing linear regression on log of sequence length.

PWMGEVBackground: Generalized Extreme Values (GEV) background for P-values

Description

Arguments

Slots