write.pairs

write.pairs-method

write.pairs,cobindr-method


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



    path to file. If filename is 'NULL' a filename is generated based on
    the name of the object of class "cobindr".    
  

file


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

background


Function writes the results of findPairs() as a tab-separated file. The file
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