Mercurial > repos > lain > xseekerpreparator


INTRODUCTION
=====
This file describes the format of the database generated by XSeeker
Preprocessor. This format will evolve in the future to fit users
wanted features. That's why there is a history of versions numbers,
describing what they brought to the sqlite file, and how it was usefull.

The first version (the older one) is at the bottom of this file, and the
modifications provided by the newest versions are on top of the file.


VERSION 1.3.0
=====
add an option to use the provided column as a class


VERSION 1.1.2
=====
add missing mz_tab_info$group_length field to produce mzTab

VERSION 1.1.1
=====
add missing mz_tab_info$dataset_path field to produce mzTab


VERSION 1.1.0
=====
Summary:
 - The field `mz_tab_info` was added in new table smol_xcms_set.

smol_xcms_set table added
-----
This table contains a subset of the original ms file.

mz_tab_info field added to smol_xcms_set
-----
This field contains five subfields:
 - sampclass ;
 - sampnames ;
 - rtmed ;
 - mzmed ;
 - smallmolecule_abundance_assay .

These fields were added after users asked to export data from XSeeker
in mzTab files.
XCMS has some functions to extract sampclass, sampnames, rtmed, mzmed
and smallmolecule_abundance_assay from xcms set. Then, they are used
in the mz tab creation process, but we didn't want to keep the whole
xcmsset object. So we used the original code from XCMS and modified it
a little bit, justifying the extraction of these new fields.


VERSION 1.0.0
=====


DATABASE
-----

### SAMPLE

#### RAW
This structure is an epurated and enriched version of the original
rdata, saved as a compressed env:
`blob::blob(fst::compress_fst(serialize(raw, NULL), compression=100))`

The fields contained in the env are as follow:

##### variableMetadata

##### tic

##### mz

##### scanindex

##### scantime

##### intensity

##### polarity

##### sample_name

##### dataset_path

##### process_params

##### enriched_rdata

##### enriched_rdata_version

##### tool_name

##### enriched_rdata_doc
author	lain
date	Tue, 18 Oct 2022 12:57:28 +0000
parents	a174cbbb12dd
children	ce94e7a141bb