PTM_MarkerFinder_util

<code>PTM_MarkerFinder_util</code> is a utility function for <code>PTM_MarkerFinder</code>.

Helps with quality checks, visualizations
and analysis of mass spectrometry data, coming from proteomics
experiments. The package is developed, tested and used at the Functional
Genomics Center Zurich <https://fgcz.ch>. We use this package
mainly for prototyping, teaching, and having fun with proteomics data.
But it can also be used to do data analysis for small scale data sets.

Christian Panse

protViz

Visualizing and Analyzing Mass Spectrometry Related Data in
Proteomics

Jonas Grossmann

Simon Barkow-Oesterreicher

PTM_MarkerFinder_util function

<dl>
 <dt>dataFileName</dt>
<dd>RData file name without 'RData' ending.</dd>
 <dt>mZmarkerIons</dt>
<dd>A double vector of the m/z patterns which should be searched.</dd>
 <dt>minMarkerIntensityRatio</dt>
<dd>The marker ions 
intencity percentage compared to the sum of all peak 
intensities.</dd>
 <dt>minNumberIons</dt>
<dd>Minimal number of marker ions to 
be found for further analysis.</dd>
 <dt>itol_ppm</dt>
<dd>The ion tolerance of the marker ions 
in ppm. default is set to 10ppm.</dd> <dt>write_csv</dt>
<dd>boolean.</dd>
</dl>

Arguments

Paolo Nanni, Christian Panse 2012-2013;

Author

<code>PTM_MarkerFinder_util</code> is a utility function for <code>PTM_MarkerFinder</code>.

PTM MarkerFinder util plot — PTM_MarkerFinder_util

<dl>


 <dt>dataFileName</dt>
<dd>RData file name without 'RData' ending.</dd>


 <dt>mZmarkerIons</dt>
<dd>A double vector of the m/z patterns which should be searched.</dd>


 <dt>minMarkerIntensityRatio</dt>
<dd>The marker ions 
intencity percentage compared to the sum of all peak 
intensities.</dd>


 <dt>minNumberIons</dt>
<dd>Minimal number of marker ions to 
be found for further analysis.</dd>


 <dt>itol_ppm</dt>
<dd>The ion tolerance of the marker ions 
in ppm. default is set to 10ppm.</dd>



 <dt>write_csv</dt>
<dd>boolean.</dd>


</dl>

Paolo Nanni, Christian Panse 2012-2013;

PTM_MarkerFinder_util: PTM MarkerFinder util plot

Description

Usage

Arguments

Author

Details