3 Performing Taxonomically Informed Metabolite Annotation
Adriano Rutz
2024-11-22
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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#> 2024-11-22 10:52:47 Loading default params
#> 2024-11-22 10:52:47 All params
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#> 2024-11-22 10:52:47 Changing params
#> 2024-11-22 10:52:47 Changing filenames
#> 2024-11-22 10:52:48 Exporting params ...
#> ● completed target par_usr_wei_ann [0.467 seconds, 1.739 kilobytes]
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#> ▶ dispatched target ann_pre
#> 2024-11-22 10:52:48 Loading files ...
#> 2024-11-22 10:52:48 ... components
#> 2024-11-22 10:52:48 ... edges
#> 2024-11-22 10:52:48 ... structure-organism pairs
#> 2024-11-22 10:52:53 ... canopus
#> 2024-11-22 10:52:53 ... formula
#> 2024-11-22 10:52:53 ... annotations
#> 2024-11-22 10:52:55 Got c("ISDB", "TIMA MS1") initial annotations
#> 2024-11-22 10:52:55 Got c(976, 289567) initial annotations
#> 2024-11-22 10:52:56 Re-arranging annotations
#> 2024-11-22 10:52:58 adding biological organism metadata
#> 2024-11-22 10:52:58 performing taxonomically informed scoring
#> 2024-11-22 10:52:58 filtering top 3 candidates and keeping only MS1 candidates with minimum
#> 0 biological score
#> OR 0 chemical score
#>
#> 2024-11-22 10:52:58 adding "notClassified"
#>
#> 2024-11-22 10:52:59 calculating biological score at all levels ...
#>
#> 2024-11-22 10:52:59 ... domain
#>
#> 2024-11-22 10:52:59 ... kingdom
#>
#> 2024-11-22 10:52:59 ... phylum
#>
#> 2024-11-22 10:52:59 ... class
#>
#> 2024-11-22 10:52:59 ... order
#>
#> 2024-11-22 10:52:59 ... family
#>
#> 2024-11-22 10:52:59 ... tribe
#>
#> 2024-11-22 10:52:59 ... genus
#>
#> 2024-11-22 10:52:59 ... species
#>
#> 2024-11-22 10:53:00 ... varietas
#>
#> 2024-11-22 10:53:00 ... keeping best biological score
#>
#> 2024-11-22 10:53:01 ... calculating weighted biological score
#>
#> 2024-11-22 10:53:01 taxonomically informed scoring led to
#> 47463 annotations reranked at the kingdom level,
#> 47000 annotations reranked at the phylum level,
#> 39309 annotations reranked at the class level,
#> 11409 annotations reranked at the order level,
#> 9386 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)
#> 2024-11-22 10:53:02 calculating chemical consistency
#> features with at least 2 neighbors ...
#>
#> 2024-11-22 10:53:02 ... among all edges ...
#>
#> 2024-11-22 10:53:02 ... at the (classyfire) kingdom level
#>
#> 2024-11-22 10:53:02 ... at the (NPC) pathway level
#>
#> 2024-11-22 10:53:02 ... at the (classyfire) superclass level
#>
#> 2024-11-22 10:53:02 ... at the (NPC) superclass level
#>
#> 2024-11-22 10:53:03 ... at the (classyfire) class level
#>
#> 2024-11-22 10:53:04 ... at the (NPC) class level
#>
#> 2024-11-22 10:53:05 ... at the (classyfire) parent level
#>
#> 2024-11-22 10:53:06 splitting already computed predictions
#>
#> 2024-11-22 10:53:07 joining all except -1 together
#>
#> 2024-11-22 10:53:09 adding dummy consistency for features
#> with less than 2 neighbors
#>
#> 2024-11-22 10:53:09 adding already computed predictions back
#>
#> 2024-11-22 10:53:11 calculating chemical score at all levels ...
#>
#> 2024-11-22 10:53:11 ... (classyfire) kingdom
#>
#> 2024-11-22 10:53:11 ... (NPC) pathway
#>
#> 2024-11-22 10:53:11 ... (classyfire) superclass
#>
#> 2024-11-22 10:53:11 ... (NPC) superclass
#>
#> 2024-11-22 10:53:11 ... (classyfire) class
#>
#> 2024-11-22 10:53:11 ... (NPC) class
#>
#> 2024-11-22 10:53:11 ... (classyfire) parent
#>
#> 2024-11-22 10:53:11 ... keeping best chemical score
#>
#> 2024-11-22 10:53:11 ... calculating weighted chemical score
#>
#> 2024-11-22 10:53:12 chemically informed scoring led to
#> 36547 annotations reranked at the (classyfire) kingdom level,
#> 24111 annotations reranked at the (NPC) pathway level,
#> 17683 annotations reranked at the (classyfire) superclass level,
#> 10017 annotations reranked at the (NPC) superclass level,
#> 17683 annotations reranked at the (classyfire) class level,
#> 9704 annotations reranked at the (NPC) class level, and
#> 9175 annotations reranked at the (classyfire) parent level.
#> WITHOUT TAKING CONSISTENCY SCORE INTO ACCOUNT!
#> 2024-11-22 10:53:12 Keeping high confidence candidates only...
#> 2024-11-22 10:53:12 Removed 289254 low confidence candidates out of the 291283 total ones.
#> 2024-11-22 10:53:12 2029 high confidence candidates remaining.
#> 2024-11-22 10:53:13 adding initial metadata (RT, etc.) and simplifying columns
#>
#> 2024-11-22 10:53:13 adding references
#>
#> 2024-11-22 10:53:15 selecting columns to export
#>
#> 2024-11-22 10:53:15 adding consensus again to droped candidates
#>
#> 2024-11-22 10:53:17 Exporting ...
#> Directory data/processed/241122_105317_example created.
#> 2024-11-22 10:53:17 ... path to used parameters is data/processed/241122_105317_example
#> 2024-11-22 10:53:17 ... path to used parameters is data/processed/241122_105317_example
#> 2024-11-22 10:53:17 ... path to export is data/processed/241122_105317_example/example_results.tsv
#> ● completed target ann_pre [29.332 seconds, 2.331 megabytes]
#> ▶ ended pipeline [33.206 seconds]
#> The final exported file is formatted in order to be easily imported in Cytoscape to further explore your data!
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