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
105
|
<HTML>
<HEAD>
<TITLE>AdditiveSeries</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">AdditiveSeries </div> </div>
</div><!--header-->
<div class="contents">
<div class="textblock"><p>Computes an additive series to quantify a peptide in a set of samples. </p>
<center></center><center><table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> AdditiveSeries <img class="formulaInl" alt="$ \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_FeatureFinderCentroided.html">FeatureFinderCentroided</a> </td><td valign="middle" align="center" rowspan="2">- </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_IDMapper.html">IDMapper</a> </td></tr>
</table>
</center><p> This module computes an additive series for an absolute quantification of a peptide in a set of samples. The output consists of a GNUplot script which can be used to visualize the results and some XML output for further processing.</p>
<p>In this version, the application computes the additive series as a ratio of the intensities of two different peptides. One of these peptides serves as internal standard for calibration.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
AdditiveSeries -- Computes an additive series to quantify a peptide in a set of samples.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
AdditiveSeries <options>
Options (mandatory options marked with '*'):
-in <files>* Input files separated by blanks (valid formats: 'featureXML')
-out <file>* Output XML file containg regression line and confidence interval (valid
formats: 'XML')
-mz_tolerance <tol> Tolerance in m/z dimension (default: '1')
-rt_tolerance <tol> Tolerance in RT dimension (default: '1')
-concentrations <concentrations>* List of spiked concentrations
-feature_rt <rt> RT position of the feature (default: '-1')
-feature_mz <mz> M/z position of the feature (default: '-1')
-standard_rt <rt> RT position of the standard (default: '-1')
-standard_mz <mz> M/z position of the standard (default: '-1')
GNUplot options:
-plot:write_gnuplot_output Flag that activates the GNUplot output
-plot:out_gp <name> Base file name (3 files with different extensions are created)
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)
</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">+AdditiveSeries</span><span class="node_description">Computes an additive series to quantify a peptide in a set of samples.</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 'AdditiveSeries'</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 files separated by blanks</span><span class="item_tags">input file</span><span class="item_restrictions">*.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 XML file containg regression line and confidence interval</span><span class="item_tags">output file</span><span class="item_restrictions">*.XML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">mz_tolerance</span><span class="item_value">1</span>
<span class="item_description">Tolerance in m/z dimension</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">rt_tolerance</span><span class="item_value">1</span>
<span class="item_description">Tolerance in RT dimension</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">concentrations</span><span class="item_value">[]</span>
<span class="item_description">List of spiked concentrations</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">feature_rt</span><span class="item_value">-1</span>
<span class="item_description">RT position of the feature</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">feature_mz</span><span class="item_value">-1</span>
<span class="item_description">m/z position of the feature</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">standard_rt</span><span class="item_value">-1</span>
<span class="item_description">RT position of the standard</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">standard_mz</span><span class="item_value">-1</span>
<span class="item_description">m/z position of the standard</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;">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">+++plot</span><span class="node_description">GNUplot options</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">write_gnuplot_output</span><span class="item_value">false</span>
<span class="item_description">Flag that activates the GNUplot output</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">out_gp</span><span class="item_value"></span>
<span class="item_description">base file name (3 files with different extensions are created)</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>
|
