3 Performing Taxonomically Informed Metabolite Annotation
Adriano Rutz
2024-12-18
Source:vignettes/articles/III-processing.Rmd
III-processing.RmdThis vignette describes how Taxonomically Informed Metabolite Annotation is performed. If you followed all previous steps successfully, this should be a piece of cake, you deserve it!
targets::tar_make(names = tidyselect::matches("ann_pre$"))
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#> 2024-12-18 14:38:02 Loading default params
#> 2024-12-18 14:38:02 All params
#> 2024-12-18 14:38:02 Small params
#> 2024-12-18 14:38:02 Changing params
#> 2024-12-18 14:38:02 Changing filenames
#> 2024-12-18 14:38:02 Exporting params ...
#> ● completed target par_usr_wei_ann [0.296 seconds, 1.739 kilobytes]
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#> ▶ dispatched target ann_pre
#> 2024-12-18 14:38:03 Loading files ...
#> 2024-12-18 14:38:03 ... components
#> 2024-12-18 14:38:03 ... edges
#> 2024-12-18 14:38:03 ... structure-organism pairs
#> 2024-12-18 14:38:07 ... canopus
#> 2024-12-18 14:38:07 ... formula
#> 2024-12-18 14:38:07 ... annotations
#> 2024-12-18 14:38:09 Got c("ISDB", "MassBank - 2024.06", "TIMA MS1") initial annotations
#> 2024-12-18 14:38:09 Got c(976, 59, 289553) initial annotations
#> 2024-12-18 14:38:09 Re-arranging annotations
#> 2024-12-18 14:38:11 adding biological organism metadata
#> 2024-12-18 14:38:11 performing taxonomically informed scoring
#> 2024-12-18 14:38:11 filtering top 3 candidates and keeping only MS1 candidates with minimum
#> 0 biological score
#> OR 0 chemical score
#>
#> 2024-12-18 14:38:11 adding "notClassified"
#>
#> 2024-12-18 14:38:12 calculating biological score at all levels ...
#>
#> 2024-12-18 14:38:12 ... domain
#>
#> 2024-12-18 14:38:12 ... kingdom
#>
#> 2024-12-18 14:38:12 ... phylum
#>
#> 2024-12-18 14:38:12 ... class
#>
#> 2024-12-18 14:38:12 ... order
#>
#> 2024-12-18 14:38:12 ... family
#>
#> 2024-12-18 14:38:12 ... tribe
#>
#> 2024-12-18 14:38:12 ... genus
#>
#> 2024-12-18 14:38:12 ... species
#>
#> 2024-12-18 14:38:13 ... varietas
#>
#> 2024-12-18 14:38:13 ... keeping best biological score
#>
#> 2024-12-18 14:38:14 ... calculating weighted biological score
#>
#> 2024-12-18 14:38:14 taxonomically informed scoring led to
#> 47459 annotations reranked at the kingdom level,
#> 46996 annotations reranked at the phylum level,
#> 39311 annotations reranked at the class level,
#> 11410 annotations reranked at the order level,
#> 9387 annotations reranked at the family level,
#> 1538 annotations reranked at the tribe level,
#> 1220 annotations reranked at the genus level,
#> 464 annotations reranked at the species level,
#> and 0 annotations reranked at the variety level.
#> WITHOUT TAKING CONSISTENCY SCORE INTO ACCOUNT! (for later predictions)
#> 2024-12-18 14:38:15 calculating chemical consistency
#> features with at least 2 neighbors ...
#>
#> 2024-12-18 14:38:15 ... among all edges ...
#>
#> 2024-12-18 14:38:15 ... at the (classyfire) kingdom level
#>
#> 2024-12-18 14:38:15 ... at the (NPC) pathway level
#>
#> 2024-12-18 14:38:15 ... at the (classyfire) superclass level
#>
#> 2024-12-18 14:38:15 ... at the (NPC) superclass level
#>
#> 2024-12-18 14:38:16 ... at the (classyfire) class level
#>
#> 2024-12-18 14:38:16 ... at the (NPC) class level
#>
#> 2024-12-18 14:38:18 ... at the (classyfire) parent level
#>
#> 2024-12-18 14:38:19 splitting already computed predictions
#>
#> 2024-12-18 14:38:19 joining all except -1 together
#>
#> 2024-12-18 14:38:21 adding dummy consistency for features
#> with less than 2 neighbors
#>
#> 2024-12-18 14:38:21 adding already computed predictions back
#>
#> 2024-12-18 14:38:23 calculating chemical score at all levels ...
#>
#> 2024-12-18 14:38:23 ... (classyfire) kingdom
#>
#> 2024-12-18 14:38:23 ... (NPC) pathway
#>
#> 2024-12-18 14:38:23 ... (classyfire) superclass
#>
#> 2024-12-18 14:38:23 ... (NPC) superclass
#>
#> 2024-12-18 14:38:23 ... (classyfire) class
#>
#> 2024-12-18 14:38:23 ... (NPC) class
#>
#> 2024-12-18 14:38:23 ... (classyfire) parent
#>
#> 2024-12-18 14:38:23 ... keeping best chemical score
#>
#> 2024-12-18 14:38:24 ... calculating weighted chemical score
#>
#> 2024-12-18 14:38:24 chemically informed scoring led to
#> 36533 annotations reranked at the (classyfire) kingdom level,
#> 24002 annotations reranked at the (NPC) pathway level,
#> 17902 annotations reranked at the (classyfire) superclass level,
#> 10188 annotations reranked at the (NPC) superclass level,
#> 17902 annotations reranked at the (classyfire) class level,
#> 9871 annotations reranked at the (NPC) class level, and
#> 9388 annotations reranked at the (classyfire) parent level.
#> WITHOUT TAKING CONSISTENCY SCORE INTO ACCOUNT!
#> 2024-12-18 14:38:24 Keeping high confidence candidates only...
#> 2024-12-18 14:38:24 Removed 289266 low confidence candidates out of the 291298 total ones.
#> 2024-12-18 14:38:24 2032 high confidence candidates remaining.
#> 2024-12-18 14:38:25 adding initial metadata (RT, etc.) and simplifying columns
#>
#> 2024-12-18 14:38:25 adding references
#>
#> 2024-12-18 14:38:27 selecting columns to export
#>
#> 2024-12-18 14:38:27 adding consensus again to droped candidates
#>
#> 2024-12-18 14:38:29 Exporting ...
#> Directory data/processed/241218_143829_example created.
#> 2024-12-18 14:38:29 ... path to used parameters is data/processed/241218_143829_example
#> 2024-12-18 14:38:29 ... path to used parameters is data/processed/241218_143829_example
#> 2024-12-18 14:38:29 ... path to export is data/processed/241218_143829_example/example_results.tsv
#> ● completed target ann_pre [26.24 seconds, 2.332 megabytes]
#> ▶ ended pipeline [30.069 seconds]
#> The final exported file is formatted in order to be easily imported in Cytoscape to further explore your data!
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