Tengeler2020 rowData has some families and genera with number suffix

[RiboRings]

Hi!

The Tengeler2020 dataset contains some families and genera in the rowData with number suffixes. It looks like they were used to make features unique, but probably they should be removed from the taxonomic ranks. I checked the original biom file and the number suffixes are also there, so it does not seem to be an issue with importing.

Example:

library(mia)

data("Tengeler2020", package = "mia")
tse <- Tengeler2020

apply(rowData(tse), 2L, function(col) col[grepl("_\\d$", col)])

# $Kingdom
# named character(0)
#
# $Phylum
# named character(0)
#
# $Class
# named character(0)
#
# $Order
# named character(0)
#
# $Family
# Clostridium_sensu_stricto_1 
#          "Clostridiaceae_1" 
#
# $Genus
#                Ruminococcus_1                 Coprococcus_2                Ruminococcus_2 
#              "Ruminococcus_1"               "Coprococcus_2"              "Ruminococcus_2" 
#           Ruminiclostridium_5   Clostridium_sensu_stricto_1           Ruminiclostridium_9 
#         "Ruminiclostridium_5" "Clostridium_sensu_stricto_1"         "Ruminiclostridium_9" 

[antagomir]

If it is the original data file and publication then I would avoid data manipulation. We can update example data set if this is problematic for some cases.