get.pairs

get.pairs-method

get.pairs,cobindr-method


    an object of the class "cobindr", which holds all necessary
    information about the sequences and the predicted binding sites.



    logical flag. If background is 'TRUE' the pairs found in the
    background sequences are used.
  

background


Function returns the results of findPairs() as a data frame. The data.frame consists of 6 columns, namely
<ul>
<li>a unique id for each pair,
  </li>
<li>the unique id of the sequence, where the pair was found,
  </li>
<li>the names of the corresponding PFMs,
  </li>
<li>the unique id for each PFM, and
  </li>
<li>the distance window in which the pair occurs.
</li>
</ul>


Finding and analysing co-occuring motifs of transcription
factor binding sites in groups of genes

Manuela Benary

cobindR

Finding Co-occuring motifs of transcription factor binding sites

get.pairs function

an object of the class "cobindr", which holds all necessary
    information about the sequences and the predicted binding sites.

logical flag. If background is 'TRUE' the pairs found in the
    background sequences are used.

Function returns the results of findPairs() as a data frame. The data.frame consists of 6 columns, namely
<ul><li>a unique id for each pair,</li></ul>
  <item>the unique id of the sequence, where the pair was found,</item>
  <item>the names of the corresponding PFMs,</item>
  <item>the unique id for each PFM, and</item>
  <item>the distance window in which the pair occurs.</item>

get.pairs: function to get output of findPairs

Description

Usage

Arguments

See Also