Mercurial > repos > lecorguille > xcms_fillpeaks

comparison test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html @ 26:bb9ee352fce0 draft

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author workflow4metabolomics
date Mon, 11 Sep 2023 09:15:33 +0000
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25:26d77e9ceb49 26:bb9ee352fce0
1 <!DOCTYPE html>
2 <HTML lang='en'>
3 <HEAD>
4 <meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />
5 <title>[W4M] XCMS analysis summary</title>
6 <style>
7 table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }
8 td, th { padding: 5px; padding-right: 12px; }
9 th { background: #898989; text-align:left;color: white;}
10 h2 { color: #FFA212; }
11 ul li { margin-bottom:10px; }
12 </style>
13 </HEAD>
14 <BODY>
15 <div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>
16 By: planemo@galaxyproject.org -
17 Date: 230525-08:53:25
18 </div>
19 <h2>Samples used:</h2>
20 <div><table>
21 <tr><th>sample</th><th>filename</th></tr>
22 <tr><td>ko15</td><td>ko15.CDF</td></tr><tr><td>ko16</td><td>ko16.CDF</td></tr><tr><td>wt15</td><td>wt15.CDF</td></tr><tr><td>wt16</td><td>wt16.CDF</td></tr>
23 </table>
24
25 </div>
26 <h2>Function launched:</h2>
27 <div><table>
28 <tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>
29 <tr><td>Mon May 11 09:37:30 2020</td><td>Peak detection</td><td colspan='2'><pre>
30 Object of class: CentWaveParam
31 Parameters:
32 ppm: 25
33 peakwidth: 20, 50
34 snthresh: 10
35 prefilter: 3, 100
36 mzCenterFun: wMean
37 integrate: 1
38 mzdiff: -0.001
39 fitgauss: FALSE
40 noise: 0
41 verboseColumns: FALSE
42 roiList length: 0
43 firstBaselineCheck TRUE
44 roiScales length: 0
45 </pre></td></tr>
46 <tr><td>Mon May 11 09:37:49 2020</td><td>Peak grouping</td><td colspan='2'><pre>
47 Object of class: PeakDensityParam
48 Parameters:
49 sampleGroups: character of length 4
50 bw: 5
51 minFraction: 0.3
52 minSamples: 1
53 binSize: 0.01
54 maxFeatures: 50
55 </pre></td></tr>
56 <tr><td>Mon May 11 09:38:08 2020</td><td>Retention time correction</td><td colspan='2'><pre>
57 Object of class: PeakGroupsParam
58 Parameters:
59 minFraction: 0.85
60 extraPeaks: 1
61 smooth: loess
62 span: 0.2
63 family: gaussian
64 subset:
65 number of peak groups: 53
66 </pre></td></tr>
67 <tr><td>Mon May 11 09:38:09 2020</td><td>Peak grouping</td><td colspan='2'><pre>
68 Object of class: PeakDensityParam
69 Parameters:
70 sampleGroups: character of length 4
71 bw: 20
72 minFraction: 0.4
73 minSamples: 1
74 binSize: 0.25
75 maxFeatures: 50
76 </pre></td></tr>
77 <tr><td>Mon May 11 09:38:18 2020</td><td>Missing peak filling</td><td colspan='2'><pre>
78 Object of class: FillChromPeaksParam
79 Parameters:
80 expandMz: 0
81 expandRt: 0
82 ppm: 0
83 </pre></td></tr>
84 </table>
85 <br/><sup>***</sup>timestamp format: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss
86 </div>
87 <h2>Informations about the XCMSnExp object:</h2>
88 <div><pre>
89 MSn experiment data ("XCMSnExp")
90 Object size in memory: 1.55 Mb
91 - - - Spectra data - - -
92 MS level(s): 1
93 Number of spectra: 5112
94 MSn retention times: 41:38 - 75:7 minutes
95 - - - Processing information - - -
96 Data loaded [Mon May 11 09:37:30 2020]
97 MSnbase version: 2.10.1
98 - - - Meta data - - -
99 phenoData
100 rowNames: 1 2 3 4
101 varLabels: sample_name sample_group
102 varMetadata: labelDescription
103 Loaded from:
104 [1] ko15.CDF... [4] wt16.CDF
105 Use 'fileNames(.)' to see all files.
106 protocolData: none
107 featureData
108 featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)
109 fvarLabels: fileIdx spIdx ... spectrum (31 total)
110 fvarMetadata: labelDescription
111 experimentData: use 'experimentData(object)'
112 - - - xcms preprocessing - - -
113 Chromatographic peak detection:
114 method: centWave
115 15405 peaks identified in 4 samples.
116 On average 3851 chromatographic peaks per sample.
117 Alignment/retention time adjustment:
118 method: peak groups
119 Correspondence:
120 method: chromatographic peak density
121 6349 features identified.
122 Median mz range of features: 0
123 Median rt range of features: 0
124 6154 filled peaks (on average 1538.5 per sample).
125 </pre></div>
126 <h2>Informations about the xcmsSet object:</h2>
127 <div><pre>
128 An "xcmsSet" object with 4 samples
129
130 Time range: 2509.2-4481.8 seconds (41.8-74.7 minutes)
131 Mass range: 200.1-600 m/z
132 Peaks: 15405 (about 3851 per sample)
133 Peak Groups: 6349
134 Sample classes: KO, WT
135
136 Feature detection:
137 o Peak picking performed on MS1.
138 o Scan range limited to 1 - 1278
139 Profile settings: method = bin
140 step = 0.1
141
142 Memory usage: 3.98 MB
143 </pre></div>
144 <h2>Citations:</h2>
145 <div><ul>
146 <li>To cite the <b>XCMS</b> package in publications use:
147 <ul>
148 <li>Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and Siuzdak, G.XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)</li>
149 <li>Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)</li>
150 <li>H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)</li>
151 </ul>
152 </li>
153 <li>To cite the <b>CAMERA</b> package in publications use:
154 <ul>
155 <li>Kuhl, C., Tautenhahn, R., Boettcher, C., Larson, T. R. and Neumann,S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84:283-289 (2012)</li>
156 </ul>
157 </li>
158 <li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:
159 <ul>
160 <li>Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics doi:10.1093/bioinformatics/btu813</li>
161 </ul>
162 </li>
163 </ul></div>
164 </BODY>
165 </HTML>