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comparison test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html @ 15:97ca0321931b draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
author lecorguille
date Tue, 18 Sep 2018 16:14:05 -0400
parents 27e7da5f6848
children 08f5203ef8c1
comparison
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14:4c757d1ba7b4 15:97ca0321931b
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><th>md5sum<sup>*</sup></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><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>
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 <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.
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 rowspan='4'>170203-11:04:42</td><td rowspan='4'>xcmsSet</td> 27 <tr><td>Wed Feb 7 11:15:25 2018</td><td>Peak detection</td><td colspan='2'><pre>
28 <td>nSlaves</td><td>1</td></tr> 28 Object of class: CentWaveParam
29 <tr><td>method</td><td>centWave</td></tr> 29 Parameters:
30 <tr><td>ppm</td><td>25</td></tr> 30 ppm: 25
31 <tr><td>peakwidth</td><td>2050</td></tr> 31 peakwidth: 20, 50
32 <tr><td rowspan='4'>170203-11:05:21</td><td rowspan='4'>xcmsSet</td> 32 snthresh: 10
33 <td>nSlaves</td><td>1</td></tr> 33 prefilter: 3, 100
34 <tr><td>method</td><td>centWave</td></tr> 34 mzCenterFun: wMean
35 <tr><td>ppm</td><td>25</td></tr> 35 integrate: 1
36 <tr><td>peakwidth</td><td>2050</td></tr> 36 mzdiff: -0.001
37 <tr><td rowspan='4'>170203-11:06:21</td><td rowspan='4'>xcmsSet</td> 37 fitgauss: FALSE
38 <td>nSlaves</td><td>1</td></tr> 38 noise: 0
39 <tr><td>method</td><td>centWave</td></tr> 39 verboseColumns: FALSE
40 <tr><td>ppm</td><td>25</td></tr> 40 roiList length: 0
41 <tr><td>peakwidth</td><td>2050</td></tr> 41 firstBaselineCheck TRUE
42 <tr><td rowspan='4'>170203-11:06:59</td><td rowspan='4'>xcmsSet</td> 42 roiScales length: 0
43 <td>nSlaves</td><td>1</td></tr> 43 </pre></td></tr>
44 <tr><td>method</td><td>centWave</td></tr> 44 <tr><td>Mon Feb 12 15:31:11 2018</td><td>Peak grouping</td><td colspan='2'><pre>
45 <tr><td>ppm</td><td>25</td></tr> 45 Object of class: PeakDensityParam
46 <tr><td>peakwidth</td><td>2050</td></tr> 46 Parameters:
47 <tr><td rowspan='6'>170203-14:38:53</td><td rowspan='6'>group</td> 47 sampleGroups: character of length 4
48 <td>method</td><td>density</td></tr> 48 bw: 30
49 <tr><td>sleep</td><td>0.001</td></tr> 49 minFraction: 0.8
50 <tr><td>minfrac</td><td>0.3</td></tr> 50 minSamples: 1
51 <tr><td>bw</td><td>5</td></tr> 51 binSize: 0.25
52 <tr><td>mzwid</td><td>0.01</td></tr> 52 maxFeatures: 50
53 <tr><td>max</td><td>50</td></tr> 53 </pre></td></tr>
54 <tr><td rowspan='7'>170203-14:51:16</td><td rowspan='7'>retcor</td> 54 <tr><td>Mon Feb 12 15:31:19 2018</td><td>Retention time correction</td><td colspan='2'><pre>
55 <td>method</td><td>peakgroups</td></tr> 55 Object of class: PeakGroupsParam
56 <tr><td>smooth</td><td>loess</td></tr> 56 Parameters:
57 <tr><td>extra</td><td>1</td></tr> 57 minFraction: 0.85
58 <tr><td>missing</td><td>1</td></tr> 58 extraPeaks: 1
59 <tr><td>span</td><td>0.2</td></tr> 59 smooth: loess
60 <tr><td>family</td><td>gaussian</td></tr> 60 span: 0.2
61 <tr><td>plottype</td><td>deviation</td></tr> 61 family: gaussian
62 <tr><td rowspan='6'>170203-15:27:58</td><td rowspan='6'>group</td> 62 number of peak groups: 125
63 <td>method</td><td>density</td></tr> 63 </pre></td></tr>
64 <tr><td>sleep</td><td>0.001</td></tr> 64 <tr><td>Mon Feb 12 15:31:27 2018</td><td>Peak grouping</td><td colspan='2'><pre>
65 <tr><td>minfrac</td><td>0.3</td></tr> 65 Object of class: PeakDensityParam
66 <tr><td>bw</td><td>5</td></tr> 66 Parameters:
67 <tr><td>mzwid</td><td>0.01</td></tr> 67 sampleGroups: character of length 4
68 <tr><td>max</td><td>50</td></tr> 68 bw: 20
69 <tr><td rowspan='5'>170203-15:44:50</td><td rowspan='5'>fillPeaks</td> 69 minFraction: 0.4
70 <td>method</td><td>chrom</td></tr> 70 minSamples: 1
71 <tr><td>convertRTMinute</td><td>FALSE</td></tr> 71 binSize: 0.25
72 <tr><td>numDigitsMZ</td><td>4</td></tr> 72 maxFeatures: 50
73 <tr><td>numDigitsRT</td><td>1</td></tr> 73 </pre></td></tr>
74 <tr><td>intval</td><td>into</td></tr> 74 <tr><td>Wed Feb 14 09:55:13 2018</td><td>Missing peak filling</td><td colspan='2'><pre>
75 Object of class: FillChromPeaksParam
76 Parameters:
77 expandMz: 0
78 expandRt: 0
79 ppm: 0
80 </pre></td></tr>
75 </table> 81 </table>
76 <br/><sup>***</sup>timestamp format: yymmdd-hh:mm:ss 82 <br/><sup>***</sup>timestamp format: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss
77 </div> 83 </div>
84 <h2>Informations about the XCMSnExp object:</h2>
85 <div><pre>
86 MSn experiment data ("XCMSnExp")
87 Object size in memory: 1.36 Mb
88 - - - Spectra data - - -
89 MS level(s): 1
90 Number of spectra: 5112
91 MSn retention times: 41:33 - 75:0 minutes
92 - - - Processing information - - -
93 Concatenated [Thu Feb 8 15:36:09 2018]
94 MSnbase version: 2.4.2
95 - - - Meta data - - -
96 phenoData
97 rowNames: ./ko15.CDF ./ko16.CDF ./wt15.CDF ./wt16.CDF
98 varLabels: sample_name sample_group
99 varMetadata: labelDescription
100 Loaded from:
101 [1] ko15.CDF... [4] wt16.CDF
102 Use 'fileNames(.)' to see all files.
103 protocolData: none
104 featureData
105 featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)
106 fvarLabels: fileIdx spIdx ... spectrum (27 total)
107 fvarMetadata: labelDescription
108 experimentData: use 'experimentData(object)'
109 - - - xcms preprocessing - - -
110 Chromatographic peak detection:
111 method: centWave
112 15230 peaks identified in 4 samples.
113 On average 3808 chromatographic peaks per sample.
114 Alignment/retention time adjustment:
115 method: peak groups
116 Correspondence:
117 method: chromatographic peak density
118 6332 features identified.
119 Median mz range of features: 0
120 Median rt range of features: 0
121 5979 filled peaks (on average 1494.75 per sample).
122 </pre></div>
78 <h2>Informations about the xcmsSet object:</h2> 123 <h2>Informations about the xcmsSet object:</h2>
79 <div><pre> 124 <div><pre>
80 An "xcmsSet" object with 4 samples 125 An "xcmsSet" object with 4 samples
81 126
82 Time range: 2506-4484 seconds (41.8-74.7 minutes) 127 Time range: 2499.4-4473.6 seconds (41.7-74.6 minutes)
83 Mass range: 200.1-600 m/z 128 Mass range: 200.1-600 m/z
84 Peaks: 32720 (about 8180 per sample) 129 Peaks: 15230 (about 3808 per sample)
85 Peak Groups: 8157 130 Peak Groups: 6332
86 Sample classes: KO, WT 131 Sample classes: KO, WT
87 132
88 Peak picking was performed on MS1. 133 Feature detection:
134 o Peak picking performed on MS1.
135 o Scan range limited to 1 - 1278
89 Profile settings: method = bin 136 Profile settings: method = bin
90 step = 0.1 137 step = 0.1
91 138
92 Memory usage: 4.25 MB 139 Memory usage: 2.98 MB
93 </pre></div> 140 </pre></div>
94 <h2>Citations:</h2> 141 <h2>Citations:</h2>
95 <div><ul> 142 <div><ul>
96 <li>To cite the <b>XCMS</b> package in publications use: 143 <li>To cite the <b>XCMS</b> package in publications use:
97 <ul> 144 <ul>