1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
|
<HTML>
<HEAD>
<TITLE>InternalCalibration</TITLE>
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
<LINK HREF="style_ini.css" REL="stylesheet" TYPE="text/css">
</HEAD>
<BODY BGCOLOR="#FFFFFF">
<A href="index.html">Home</A> ·
<A href="classes.html">Classes</A> ·
<A href="annotated.html">Annotated Classes</A> ·
<A href="modules.html">Modules</A> ·
<A href="functions_func.html">Members</A> ·
<A href="namespaces.html">Namespaces</A> ·
<A href="pages.html">Related Pages</A>
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<!-- Generated by Doxygen 1.8.5 -->
</div><!-- top -->
<div class="header">
<div class="headertitle">
<div class="title">InternalCalibration </div> </div>
</div><!--header-->
<div class="contents">
<div class="textblock"><p>Performs an internal calibration on an MS experiment.</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> InternalCalibration <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_PeakPickerWavelet.html">PeakPickerWavelet</a> </td><td valign="middle" align="center" rowspan="2">any tool operating on MS peak data <br/>
(in mzML format) or feature data </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_FeatureFinderCentroided.html">FeatureFinderCentroided</a> </td></tr>
</table>
</center><p>This a simple calibration method: given a list of reference masses and an MS experiment or a feature map, the relative errors of the peaks in the data are approximated by linear regression and subtracted from the data. The user can choose whether the calibration function shall be calculated for each spectrum separately or once for the whole map. If this is done scanwise, at least two reference masses need to be present in each scan to calculate the calibration function, otherwise the spectrum can't be calibrated. For the global calibration it is also possible to use a list of (significant) peptide identifications.</p>
<dl class="section note"><dt>Note</dt><dd>The tool assumes the input data is already picked or feature maps.</dd></dl>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
InternalCalibration -- Applies an internal calibration.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
InternalCalibration <options>
This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti
on or use the --helphelp option.
Options (mandatory options marked with '*'):
-in <file>* Input peak file (valid formats: 'mzML', 'featureXML')
-out <file>* Output file (valid formats: 'mzML', 'featureXML')
-ref_peaks <file> Input file containing reference m/z values (either as textfile with one m/z per
line and no header or as idXML file) (valid formats: 'csv', 'idXML')
-type <calibration type> The kind of internal calibration that should be applied. (default: 'spectrumwise'
valid: 'spectrumwise', 'global')
-trafo <file> Output transformation file (only for global calibration) (valid formats: 'trafoXM
L')
Common TOPP options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
The following configuration subsections are valid:
- algorithm Settings for the internal calibration.
You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
Have a look at the OpenMS documentation for more information.
</pre><p> <b>INI file documentation of this tool:</b> <div class="ini_global">
<div class="legend">
<b>Legend:</b><br>
<div class="item item_required">required parameter</div>
<div class="item item_advanced">advanced parameter</div>
</div>
<div class="node"><span class="node_name">+InternalCalibration</span><span class="node_description">Applies an internal calibration.</span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:16px;">version</span><span class="item_value">1.11.1</span>
<span class="item_description">Version of the tool that generated this parameters file.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">++1</span><span class="node_description">Instance '1' section for 'InternalCalibration'</span></div>
<div class="item"><span class="item_name item_required" style="padding-left:24px;">in</span><span class="item_value"></span>
<span class="item_description">input peak file </span><span class="item_tags">input file</span><span class="item_restrictions">*.mzML,*.featureXML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">out</span><span class="item_value"></span>
<span class="item_description">output file </span><span class="item_tags">output file</span><span class="item_restrictions">*.mzML,*.featureXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">ref_peaks</span><span class="item_value"></span>
<span class="item_description">input file containing reference m/z values (either as textfile with one m/z per line and no header or as idXML file)</span><span class="item_tags">input file</span><span class="item_restrictions">*.csv,*.idXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">type</span><span class="item_value">spectrumwise</span>
<span class="item_description">The kind of internal calibration that should be applied.</span><span class="item_tags"></span><span class="item_restrictions">spectrumwise,global</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">trafo</span><span class="item_value"></span>
<span class="item_description">output transformation file (only for global calibration)</span><span class="item_tags">output file</span><span class="item_restrictions">*.trafoXML</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">log</span><span class="item_value"></span>
<span class="item_description">Name of log file (created only when specified)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">debug</span><span class="item_value">0</span>
<span class="item_description">Sets the debug level</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">threads</span><span class="item_value">1</span>
<span class="item_description">Sets the number of threads allowed to be used by the TOPP tool</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">no_progress</span><span class="item_value">false</span>
<span class="item_description">Disables progress logging to command line</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">test</span><span class="item_value">false</span>
<span class="item_description">Enables the test mode (needed for internal use only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="node"><span class="node_name">+++algorithm</span><span class="node_description">Settings for the internal calibration.</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">mz_tolerance</span><span class="item_value">1</span>
<span class="item_description">Allowed tolerance between peak and reference m/z.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">mz_tolerance_unit</span><span class="item_value">Da</span>
<span class="item_description">Unit for mz_tolerance.</span><span class="item_tags"></span><span class="item_restrictions">Da,ppm</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">rt_tolerance</span><span class="item_value">10</span>
<span class="item_description">Allowed tolerance between peak and reference rt.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div></div>
</div></div><!-- contents -->
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<TABLE width="100%" border="0">
<TR>
<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5</font></TD>
</TR>
</TABLE>
</BODY>
</HTML>
|
