Taxonomic levels Genus names at Family rank

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
25/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Stale
Tech stack
r
Domain
data

Research direction

Start by reproducing the family-level counts with getCompendium() and rowData(vcpd) using the R snippet, then compare the taxonomy source with the linked dada2-reference-databases issue. Done means determining whether names such as Anaerococcus and Finegoldia are incorrectly assigned at family rank and documenting or correcting the affected taxonomy.

Written by the indexing model from the issue text.

Description

Dear Authors,
Congrats on this huge task and thanks for creating this resource.
When exploring the data at family level, I noticed an issue regarding taxonomy that was highlighted couple of year back in the dada2 silva database. I am not sure if the source database used in this study is from this repository but there seems to be the same issue.
https://github.com/mikemc/dada2-reference-databases/issues/1

# BiocManager::install('seandavi/MicroBioMap')
library(MicroBioMap)
library(mia)
library(dplyr)
cpd <- getCompendium()
saveRDS(cpd, 'MicroBioMapDataTSE.rds')

vcpd <- mia::subsetByPrevalentFeatures(cpd, 
                                       detection=0.0001, 
                                       prevalence=0.01,
                                       as_relative = TRUE)

dplyr::count(as.data.frame(rowData(vcpd)), family)

examples of genus level names at family level are Anaerococcus, Ezakiella, Finegoldia, Parvimonas, Peptoniphilus etc

Best wishes,
Sudarshan

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R
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Forks
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