PWMCutoffBackground

PWMCutoffBackground-class


  Hit count 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

PWMCutoffBackground function

<dl>
<dt><code>bg.source</code>:</dt><dd>textual description
  of where the background distribution is derived from</dd> <dt><code>bg.cutoff</code>:</dt><dd>the cutoff score used to find
  significant motif hits (in log2 odds), either a single
  value or a vector of values</dd>
 <dt><code>bg.P</code>:</dt><dd>the
  density of significant motif hits per nucleotide in
  background</dd>
 <dt><code>pwms</code>:</dt><dd>the pwms for which the
  background has been compiled</dd>
 </dl> 

Slots

Hit count background distribution for a set of PWMs

PWMCutoffBackground: Hit count background distribution for a set of PWMs

Description

Arguments

Slots