Mercurial > repos > lain > xseekerpreparator
comparison format_versionning.MD @ 0:a174cbbb12dd draft
" master branch Updating"
| author | lain |
|---|---|
| date | Tue, 24 Nov 2020 18:55:08 +0000 |
| parents | |
| children | 2937e72e5891 |
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| -1:000000000000 | 0:a174cbbb12dd |
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| 1 | |
| 2 INTRODUCTION | |
| 3 ===== | |
| 4 This file describes the format of the database generated by XSeeker | |
| 5 Preprocessor. This format will evolve in the future to fit users | |
| 6 wanted features. That's why there is a history of versions numbers, | |
| 7 describing what they brought to the sqlite file, and how it was usefull. | |
| 8 | |
| 9 The first version (the older one) is at the bottom of this file, and the | |
| 10 modifications provided by the newest versions are on top of the file. | |
| 11 | |
| 12 | |
| 13 VERSION 1.1.2 | |
| 14 ===== | |
| 15 add missing mz_tab_info$group_length field to produce mzTab | |
| 16 | |
| 17 VERSION 1.1.1 | |
| 18 ===== | |
| 19 add missing mz_tab_info$dataset_path field to produce mzTab | |
| 20 | |
| 21 | |
| 22 VERSION 1.1.0 | |
| 23 ===== | |
| 24 Summary: | |
| 25 - The field `mz_tab_info` was added in new table smol_xcms_set. | |
| 26 | |
| 27 smol_xcms_set table added | |
| 28 ----- | |
| 29 This table contains a subset of the original ms file. | |
| 30 | |
| 31 mz_tab_info field added to smol_xcms_set | |
| 32 ----- | |
| 33 This field contains five subfields: | |
| 34 - sampclass ; | |
| 35 - sampnames ; | |
| 36 - rtmed ; | |
| 37 - mzmed ; | |
| 38 - smallmolecule_abundance_assay . | |
| 39 | |
| 40 These fields were added after users asked to export data from XSeeker | |
| 41 in mzTab files. | |
| 42 XCMS has some functions to extract sampclass, sampnames, rtmed, mzmed | |
| 43 and smallmolecule_abundance_assay from xcms set. Then, they are used | |
| 44 in the mz tab creation process, but we didn't want to keep the whole | |
| 45 xcmsset object. So we used the original code from XCMS and modified it | |
| 46 a little bit, justifying the extraction of these new fields. | |
| 47 | |
| 48 | |
| 49 VERSION 1.0.0 | |
| 50 ===== | |
| 51 | |
| 52 | |
| 53 DATABASE | |
| 54 ----- | |
| 55 | |
| 56 ### SAMPLE | |
| 57 | |
| 58 #### RAW | |
| 59 This structure is an epurated and enriched version of the original | |
| 60 rdata, saved as a compressed env: | |
| 61 `blob::blob(fst::compress_fst(serialize(raw, NULL), compression=100))` | |
| 62 | |
| 63 The fields contained in the env are as follow: | |
| 64 | |
| 65 ##### variableMetadata | |
| 66 | |
| 67 ##### tic | |
| 68 | |
| 69 ##### mz | |
| 70 | |
| 71 ##### scanindex | |
| 72 | |
| 73 ##### scantime | |
| 74 | |
| 75 ##### intensity | |
| 76 | |
| 77 ##### polarity | |
| 78 | |
| 79 ##### sample_name | |
| 80 | |
| 81 ##### dataset_path | |
| 82 | |
| 83 ##### process_params | |
| 84 | |
| 85 ##### enriched_rdata | |
| 86 | |
| 87 ##### enriched_rdata_version | |
| 88 | |
| 89 ##### tool_name | |
| 90 | |
| 91 ##### enriched_rdata_doc |