BCRANKresult-class

BCRANKresult

toptable

fname

Holds the results from running
  <code><a rd-options="BCRANK:bcrank" href="/link/bcrank?package=BCRANK&version=1.34.0&to=BCRANK%3Abcrank" data-mini-rdoc="BCRANK:bcrank::bcrank">bcrank</a></code>. Contains a number of
  <code><a rd-options="BCRANK:BCRANKsearch-class" href="/link/BCRANKsearch-class?package=BCRANK&version=1.34.0&to=BCRANK%3ABCRANKsearch-class" data-mini-rdoc="BCRANK:BCRANKsearch-class::BCRANKsearch-class">BCRANKsearch-class</a></code> object,
  one for each restart of the bcrank search.

classes

Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search

Adam Ameur

BCRANK

Predicting binding site consensus from ranked DNA sequences

BCRANKresult-class function

<dl>
    <dt><code>fname</code>:</dt><dd>the name of the fasta file used for running bcrank.</dd> <dt><code>toplist</code>:</dt><dd>a list of <code>BCRANKsearch-class</code> objects,
	  ranked by their scores.</dd> <dt><code>funCall</code>:</dt><dd>the function call that was made to bcrank.</dd> <dt><code>nrSeqs</code>:</dt><dd>number of sequences in the fasta input file.</dd> <dt><code>restarts</code>:</dt><dd>number of restarts used in the bcrank
	  search.</dd> </dl> 

Slots

<dl>
    <dt>fname</dt><dd><code>signature(object = "BCRANKmatch")</code>: Returns the
	  fasta file name.</dd> <dt>toplist</dt><dd><code>signature(object = "BCRANKmatch", i=NULL)</code>: If
	  <code>i</code> is NULL, returns a data frame containing consensus and
	  score for the results for each restart of the bcrank
	  search. Otherwise, the i'th <code>BCRANKsearch-class</code> object in
	  the toplist is returned.</dd> </dl> 

Methods

Holds the results from running
  <code><a href="bcrank" rd-options="BCRANK:bcrank">bcrank</a></code>. Contains a number of
  <code><a href="BCRANKsearch-class" rd-options="BCRANK:BCRANKsearch-class">BCRANKsearch-class</a></code> object,
  one for each restart of the bcrank search.

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BCRANKresult-class: Class "BCRANKresult"

Description

Arguments

Slots

Methods

See Also