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1
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2 INTRODUCTION
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3 =====
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4 This file describes the format of the database generated by XSeeker
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5 Preprocessor. This format will evolve in the future to fit users
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6 wanted features. That's why there is a history of versions numbers,
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7 describing what they brought to the sqlite file, and how it was usefull.
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8
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9 The first version (the older one) is at the bottom of this file, and the
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10 modifications provided by the newest versions are on top of the file.
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11
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20
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12 Also, the changelog will be mixed to this file
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13
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14
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15 VERSION 1.3.1
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16 =====
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17 bugfix in files processing, some files were not processed due to
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18 a missunderstanding of the meaning of a field in the rdata.
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19
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20
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19
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21 VERSION 1.3.0
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22 =====
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23 add an option to use the provided column as a class
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24
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25
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26 VERSION 1.1.2
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27 =====
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28 add missing mz_tab_info$group_length field to produce mzTab
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29
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30 VERSION 1.1.1
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31 =====
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32 add missing mz_tab_info$dataset_path field to produce mzTab
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33
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34
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35 VERSION 1.1.0
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36 =====
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37 Summary:
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38 - The field `mz_tab_info` was added in new table smol_xcms_set.
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39
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40 smol_xcms_set table added
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41 -----
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42 This table contains a subset of the original ms file.
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43
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44 mz_tab_info field added to smol_xcms_set
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45 -----
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46 This field contains five subfields:
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47 - sampclass ;
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48 - sampnames ;
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49 - rtmed ;
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50 - mzmed ;
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51 - smallmolecule_abundance_assay .
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52
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53 These fields were added after users asked to export data from XSeeker
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54 in mzTab files.
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55 XCMS has some functions to extract sampclass, sampnames, rtmed, mzmed
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56 and smallmolecule_abundance_assay from xcms set. Then, they are used
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57 in the mz tab creation process, but we didn't want to keep the whole
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58 xcmsset object. So we used the original code from XCMS and modified it
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59 a little bit, justifying the extraction of these new fields.
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60
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61
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62 VERSION 1.0.0
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63 =====
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64
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65
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66 DATABASE
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67 -----
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68
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69 ### SAMPLE
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70
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71 #### RAW
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72 This structure is an epurated and enriched version of the original
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73 rdata, saved as a compressed env:
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74 `blob::blob(fst::compress_fst(serialize(raw, NULL), compression=100))`
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75
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76 The fields contained in the env are as follow:
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77
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78 ##### variableMetadata
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79
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80 ##### tic
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81
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82 ##### mz
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83
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84 ##### scanindex
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85
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86 ##### scantime
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87
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88 ##### intensity
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89
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90 ##### polarity
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91
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92 ##### sample_name
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93
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94 ##### dataset_path
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95
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96 ##### process_params
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97
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98 ##### enriched_rdata
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99
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100 ##### enriched_rdata_version
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101
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102 ##### tool_name
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103
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104 ##### enriched_rdata_doc |
