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feat(mztab-m): add an mzTab-M data source and query layer - #62
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Add MzTabMSource(), which reads the small molecule features (SMF) of an mzTab-M 2.0 file and pairs them with the raw files they came from, and lp_mztab(), which selects the features to plot with a query such as "reliability <= 2". As MS-DIAL, MZmine and OpenMS all export mzTab-M, this one source covers several tools. The source extends ExternalDataSource. Assays are mapped to sample paths through their ms_run locations, matched by basename (and without the extension as a fallback). Features are annotated with the name, formula, database identifier and reliability of the SML rows that reference them; a feature claimed by several SML rows keeps the first and is flagged as ambiguous. Since one compound is often reported as several adduct features, create_compound_chromatograms() gains a key argument and the mzTab-M chromatograms are keyed by SMF_ID instead of name. The vignette now plots a real example: the HUPO-PSI MTBLS263 mzTab-M file (Progenesis QI) with its MetaboLights raw files, cut down to eight features and shipped in inst/extdata. tools/mztab rebuilds it. Bump the version to 1.1.19. Closes #51.
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Add MzTabMSource(), which reads the small molecule features (SMF) of an mzTab-M 2.0 file and pairs them with the raw files they came from, and lp_mztab(), which selects the features to plot with a query such as "reliability <= 2". As MS-DIAL, MZmine and OpenMS all export mzTab-M, this one source covers several tools.
The source extends ExternalDataSource. Assays are mapped to sample paths through their ms_run locations, matched by basename (and without the extension as a fallback). Features are annotated with the name, formula, database identifier and reliability of the SML rows that reference them; a feature claimed by several SML rows keeps the first and is flagged as ambiguous. Since one compound is often reported as several adduct features, create_compound_chromatograms() gains a key argument and the mzTab-M chromatograms are keyed by SMF_ID instead of name.
The vignette now plots a real example: the HUPO-PSI MTBLS263 mzTab-M file (Progenesis QI) with its MetaboLights raw files, cut down to eight features and shipped in inst/extdata. tools/mztab rebuilds it. Bump the version to 1.1.19.
Closes #51.