output.binding.results

output of the <code><a rd-options="" href="/link/find.binding.positions?package=spp&version=1.16.0" data-mini-rdoc="spp::find.binding.positions">find.binding.positions</a></code>

results

filename

Writes out determined binding positions into a text file. The file
 will contain a table with each row corresponding to a detected
 position, with the following columns<ul>
<li>chr: chromosome or target sequence</li>
<li>pos: position of detected binding site on the chromosome/sequence</li>
<li>score: a score reflecting magnitude of the binding</li>
<li>Evalue: E-value corresponding to the peak magnitude</li>
<li>FDR: FDR corresponding to the peak magnitude</li>
<li>enrichment.lb: lower bound of the fold-enrichment ratio</li>
<li>enrichment.mle: maximum likelihood estimate of the fold-enrichment ratio</li>
</ul>

Analysis of ChIP-seq and other functional sequencing data [Kharchenko PV (2008) <DOI:10.1038/nbt.1508>].

Peter Kharchenko

ChIP-Seq Processing Pipeline

output.binding.results function

output of the <code><a rd-options='' href='find.binding.positions'>find.binding.positions</a></code>

output.binding.results: Write out determined binding peaks into a text file table

Description

Usage

Arguments