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comparison test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html @ 26:db6549f27ad1 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8"
author workflow4metabolomics
date Tue, 12 May 2020 16:39:28 -0400
parents 08f5203ef8c1
children 018a9771de28
comparison
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25:acc66e5c23d7 26:db6549f27ad1
14 <BODY> 14 <BODY>
15 <div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1> 15 <div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>
16 </div> 16 </div>
17 <h2>Samples used:</h2> 17 <h2>Samples used:</h2>
18 <div><table> 18 <div><table>
19 <tr><th>sample</th><th>filename</th><th>md5sum<sup>*</sup></th></tr> 19 <tr><th>sample</th><th>filename</th></tr>
20 <tr><td>ko15</td><td>ko15.CDF</td><td>4698c36c0b3af007faf70975c04ccf2a</td></tr><tr><td>ko16</td><td>ko16.CDF</td><td>afaeed94ced3140bc042d5ab6aeb16c1</td></tr><tr><td>wt15</td><td>wt15.CDF</td><td>d58a27fad7c04ddddb0359ddc2b7ba68</td></tr><tr><td>wt16</td><td>wt16.CDF</td><td>29654e9f8ad48c1fbe2a41b9ba578f6e</td></tr> 20 <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>
21 </table> 21 </table>
22 <br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were changed during the process. 22
23 </div> 23 </div>
24 <h2>Function launched:</h2> 24 <h2>Function launched:</h2>
25 <div><table> 25 <div><table>
26 <tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr> 26 <tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>
27 <tr><td>Wed Feb 7 11:15:25 2018</td><td>Peak detection</td><td colspan='2'><pre> 27 <tr><td>Mon May 11 09:37:30 2020</td><td>Peak detection</td><td colspan='2'><pre>
28 Object of class: CentWaveParam 28 Object of class: CentWaveParam
29 Parameters: 29 Parameters:
30 ppm: 25 30 ppm: 25
31 peakwidth: 20, 50 31 peakwidth: 20, 50
32 snthresh: 10 32 snthresh: 10
39 verboseColumns: FALSE 39 verboseColumns: FALSE
40 roiList length: 0 40 roiList length: 0
41 firstBaselineCheck TRUE 41 firstBaselineCheck TRUE
42 roiScales length: 0 42 roiScales length: 0
43 </pre></td></tr> 43 </pre></td></tr>
44 <tr><td>Mon Feb 12 15:31:11 2018</td><td>Peak grouping</td><td colspan='2'><pre> 44 <tr><td>Mon May 11 09:37:49 2020</td><td>Peak grouping</td><td colspan='2'><pre>
45 Object of class: PeakDensityParam 45 Object of class: PeakDensityParam
46 Parameters: 46 Parameters:
47 sampleGroups: character of length 4 47 sampleGroups: character of length 4
48 bw: 30 48 bw: 5
49 minFraction: 0.8 49 minFraction: 0.3
50 minSamples: 1 50 minSamples: 1
51 binSize: 0.25 51 binSize: 0.01
52 maxFeatures: 50 52 maxFeatures: 50
53 </pre></td></tr> 53 </pre></td></tr>
54 <tr><td>Mon Feb 12 15:31:19 2018</td><td>Retention time correction</td><td colspan='2'><pre> 54 <tr><td>Mon May 11 09:38:08 2020</td><td>Retention time correction</td><td colspan='2'><pre>
55 Object of class: PeakGroupsParam 55 Object of class: PeakGroupsParam
56 Parameters: 56 Parameters:
57 minFraction: 0.85 57 minFraction: 0.85
58 extraPeaks: 1 58 extraPeaks: 1
59 smooth: loess 59 smooth: loess
60 span: 0.2 60 span: 0.2
61 family: gaussian 61 family: gaussian
62 number of peak groups: 125 62 subset:
63 number of peak groups: 53
63 </pre></td></tr> 64 </pre></td></tr>
64 <tr><td>Mon Feb 12 15:31:27 2018</td><td>Peak grouping</td><td colspan='2'><pre> 65 <tr><td>Mon May 11 09:38:09 2020</td><td>Peak grouping</td><td colspan='2'><pre>
65 Object of class: PeakDensityParam 66 Object of class: PeakDensityParam
66 Parameters: 67 Parameters:
67 sampleGroups: character of length 4 68 sampleGroups: character of length 4
68 bw: 20 69 bw: 20
69 minFraction: 0.4 70 minFraction: 0.4
70 minSamples: 1 71 minSamples: 1
71 binSize: 0.25 72 binSize: 0.25
72 maxFeatures: 50 73 maxFeatures: 50
73 </pre></td></tr> 74 </pre></td></tr>
74 <tr><td>Wed Feb 14 09:55:13 2018</td><td>Missing peak filling</td><td colspan='2'><pre> 75 <tr><td>Mon May 11 09:38:18 2020</td><td>Missing peak filling</td><td colspan='2'><pre>
75 Object of class: FillChromPeaksParam 76 Object of class: FillChromPeaksParam
76 Parameters: 77 Parameters:
77 expandMz: 0 78 expandMz: 0
78 expandRt: 0 79 expandRt: 0
79 ppm: 0 80 ppm: 0
82 <br/><sup>***</sup>timestamp format: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss 83 <br/><sup>***</sup>timestamp format: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss
83 </div> 84 </div>
84 <h2>Informations about the XCMSnExp object:</h2> 85 <h2>Informations about the XCMSnExp object:</h2>
85 <div><pre> 86 <div><pre>
86 MSn experiment data ("XCMSnExp") 87 MSn experiment data ("XCMSnExp")
87 Object size in memory: 1.41 Mb 88 Object size in memory: 1.55 Mb
88 - - - Spectra data - - - 89 - - - Spectra data - - -
89 MS level(s): 1 90 MS level(s): 1
90 Number of spectra: 5112 91 Number of spectra: 5112
91 MSn retention times: 41:33 - 75:0 minutes 92 MSn retention times: 41:38 - 75:7 minutes
92 - - - Processing information - - - 93 - - - Processing information - - -
93 Concatenated [Thu Feb 8 15:36:09 2018] 94 Data loaded [Mon May 11 09:37:30 2020]
94 MSnbase version: 2.4.2 95 MSnbase version: 2.10.1
95 - - - Meta data - - - 96 - - - Meta data - - -
96 phenoData 97 phenoData
97 rowNames: ./ko15.CDF ./ko16.CDF ./wt15.CDF ./wt16.CDF 98 rowNames: 1 2 3 4
98 varLabels: sample_name sample_group 99 varLabels: sample_name sample_group
99 varMetadata: labelDescription 100 varMetadata: labelDescription
100 Loaded from: 101 Loaded from:
101 [1] ko15.CDF... [4] wt16.CDF 102 [1] ko15.CDF... [4] wt16.CDF
102 Use 'fileNames(.)' to see all files. 103 Use 'fileNames(.)' to see all files.
103 protocolData: none 104 protocolData: none
104 featureData 105 featureData
105 featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total) 106 featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)
106 fvarLabels: fileIdx spIdx ... spectrum (27 total) 107 fvarLabels: fileIdx spIdx ... spectrum (31 total)
107 fvarMetadata: labelDescription 108 fvarMetadata: labelDescription
108 experimentData: use 'experimentData(object)' 109 experimentData: use 'experimentData(object)'
109 - - - xcms preprocessing - - - 110 - - - xcms preprocessing - - -
110 Chromatographic peak detection: 111 Chromatographic peak detection:
111 method: centWave 112 method: centWave
112 15230 peaks identified in 4 samples. 113 15405 peaks identified in 4 samples.
113 On average 3808 chromatographic peaks per sample. 114 On average 3851 chromatographic peaks per sample.
114 Alignment/retention time adjustment: 115 Alignment/retention time adjustment:
115 method: peak groups 116 method: peak groups
116 Correspondence: 117 Correspondence:
117 method: chromatographic peak density 118 method: chromatographic peak density
118 6332 features identified. 119 6349 features identified.
119 Median mz range of features: 0 120 Median mz range of features: 0
120 Median rt range of features: 0 121 Median rt range of features: 0
121 5979 filled peaks (on average 1494.75 per sample). 122 6154 filled peaks (on average 1538.5 per sample).
122 </pre></div> 123 </pre></div>
123 <h2>Informations about the xcmsSet object:</h2> 124 <h2>Informations about the xcmsSet object:</h2>
124 <div><pre> 125 <div><pre>
125 An "xcmsSet" object with 4 samples 126 An "xcmsSet" object with 4 samples
126 127
127 Time range: 2499.4-4473.6 seconds (41.7-74.6 minutes) 128 Time range: 2509.2-4481.8 seconds (41.8-74.7 minutes)
128 Mass range: 200.1-600 m/z 129 Mass range: 200.1-600 m/z
129 Peaks: 15230 (about 3808 per sample) 130 Peaks: 15405 (about 3851 per sample)
130 Peak Groups: 6332 131 Peak Groups: 6349
131 Sample classes: KO, WT 132 Sample classes: KO, WT
132 133
133 Feature detection: 134 Feature detection:
134 o Peak picking performed on MS1. 135 o Peak picking performed on MS1.
135 o Scan range limited to 1 - 1278 136 o Scan range limited to 1 - 1278
136 Profile settings: method = bin 137 Profile settings: method = bin
137 step = 0.1 138 step = 0.1
138 139
139 Memory usage: 3.11 MB 140 Memory usage: 3.98 MB
140 </pre></div> 141 </pre></div>
141 <h2>Citations:</h2> 142 <h2>Citations:</h2>
142 <div><ul> 143 <div><ul>
143 <li>To cite the <b>XCMS</b> package in publications use: 144 <li>To cite the <b>XCMS</b> package in publications use:
144 <ul> 145 <ul>