4 Performing Taxonomically Informed Metabolite Annotation
Adriano Rutz
2023-08-29
Source:vignettes/IV-processing.Rmd
IV-processing.RmdThis vignette describes how to perform Taxonomically Informed Metabolite Annotation. If you followed all previous steps successfully, this should be a piece of cake, you deserve it!
Before running the corresponding code, do not forget to modify
inst/params/user/weight_annotations.yaml.
source(file = "inst/scripts/weight_annotations.R")
#> 2023-08-29 14:12:53.448922 This script performs taxonomically informed scoring and followed by chemical consistency informed scoring
#> 2023-08-29 14:12:53.454833 Authors: AR , PMA
#>
#> 2023-08-29 14:12:53.455229 Contributors: ...
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#> ▶ start target ann_pre
#> 2023-08-29 14:13:00.510288 Loading files ...
#> 2023-08-29 14:13:00.513001 ... components
#> 2023-08-29 14:13:00.619872 ... edges
#> 2023-08-29 14:13:00.657766 ... structure-organism pairs
#> 2023-08-29 14:13:06.514085 ... annotations
#> 2023-08-29 14:13:28.274829 adding biological organism metadata
#> 2023-08-29 14:13:30.099232 performing taxonomically informed scoring
#> 2023-08-29 14:13:30.161354 filtering top 3 candidates and keeping only MS1 candidates with minimum
#> 0.5 biological score
#> OR 0.666 chemical score
#>
#> 2023-08-29 14:13:43.501027 selecting DB columns
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#> 2023-08-29 14:13:44.222037 keeping distinct candidates per taxonomical rank
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#> 2023-08-29 14:13:45.795574 calculating biological scores ...
#>
#> 2023-08-29 14:13:45.795786 ... domain
#>
#> 2023-08-29 14:13:47.77545 ... kingdom
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#> 2023-08-29 14:13:50.71623 ... phylum
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#> 2023-08-29 14:13:53.520924 ... class
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#> 2023-08-29 14:13:57.230276 ... order
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#> 2023-08-29 14:14:04.006272 ... family
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#> 2023-08-29 14:14:08.930156 ... tribe
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#> 2023-08-29 14:14:11.99058 ... genus
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#> 2023-08-29 14:14:18.009001 ... species
#>
#> 2023-08-29 14:14:26.167878 ... varietas
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#> 2023-08-29 14:14:27.572494 keeping best biological score only
#>
#> 2023-08-29 14:14:51.105946 taxonomically informed scoring led to
#> 95702 annotations reranked at the kingdom level,
#> 94484 annotations reranked at the phylum level,
#> 88995 annotations reranked at the class level,
#> 29942 annotations reranked at the order level,
#> 22805 annotations reranked at the family level,
#> 3196 annotations reranked at the tribe level,
#> 2265 annotations reranked at the genus level,
#> 826 annotations reranked at the species level,
#> and 0 annotations reranked at the variety level.
#>
#> 2023-08-29 14:14:53.025388 adding "notClassified"
#>
#> 2023-08-29 14:14:54.768526 calculating chemical consistency
#> features with at least 2 neighbors ...
#>
#> 2023-08-29 14:14:54.768765 ... among edges ...
#>
#> 2023-08-29 14:14:59.818068 ... at the (classyfire) kingdom level
#>
#> 2023-08-29 14:15:03.815033 ... at the (NPC) pathway level
#>
#> 2023-08-29 14:15:08.538888 ... at the (classyfire) superclass level
#>
#> 2023-08-29 14:15:12.751976 ... at the (NPC) superclass level
#>
#> 2023-08-29 14:15:23.575866 ... at the (classyfire) class level
#>
#> 2023-08-29 14:15:36.717266 ... at the (NPC) class level
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#> 2023-08-29 14:16:07.747641 ... at the (classyfire) parent level
#>
#> 2023-08-29 14:16:43.215121 joining all except -1 together
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#> 2023-08-29 14:16:53.257391 adding dummy consistency for features
#> with less than 2 neighbors
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#> 2023-08-29 14:16:56.649831 calculating chemical score at all levels ...
#>
#> 2023-08-29 14:16:56.650042 ... (classyfire) kingdom
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#> 2023-08-29 14:17:05.745146 ... (NPC) pathway
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#> 2023-08-29 14:17:14.410753 ... (classyfire) superclass
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#> 2023-08-29 14:17:19.668003 ... (NPC) superclass
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#> 2023-08-29 14:17:21.22134 ... (classyfire) class
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#> 2023-08-29 14:17:22.860509 ... (NPC) class
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#> 2023-08-29 14:17:23.353894 ... (classyfire) parent
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#> 2023-08-29 14:17:24.327558 ... joining best score
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#> 2023-08-29 14:17:27.831513 ... cleaning
#>
#> 2023-08-29 14:17:51.165036 chemically informed scoring led to
#> 136002 annotations reranked at the (classyfire) kingdom level,
#> 100850 annotations reranked at the (NPC) pathway level,
#> 86961 annotations reranked at the (classyfire) superclass level,
#> 61647 annotations reranked at the (NPC) superclass level,
#> 52600 annotations reranked at the (classyfire) class level,
#> 15047 annotations reranked at the (NPC) class level, and
#> 15046 annotations reranked at the (classyfire) parent level.
#>
#> 2023-08-29 14:17:56.407413 adding initial metadata (RT, etc.) and simplifying columns
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#> 2023-08-29 14:17:56.818269 adding references
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#> 2023-08-29 14:18:06.974977 selecting columns to export
#>
#> 2023-08-29 14:18:09.745539 adding consensus again to droped candidates
#>
#> 2023-08-29 14:18:33.934627 Exporting ...
#> 2023-08-29 14:18:33.942758 Directory data/processed/230829_141833_example created.
#> 2023-08-29 14:18:33.943056 ... path to used parameters is data/processed/230829_141833_example
#> 2023-08-29 14:18:33.952483 ... path to export is data/processed/230829_141833_example/annotations.tsv
#> ● built target ann_pre [5.562 minutes]
#> ▶ end pipeline [5.642 minutes]
#> 2023-08-29 14:18:34.542438 Script finished in 5.684895 minsThe final exported file is formatted in order to be easily imported in Cytoscape to further explore your data!
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