The Maaslin2 function changes several characters (e.g. semicolon, hyphen, square bracket and parenthesis) in the taxonomic names from Silva-db to a period (i.e. a .). How can this be avoided?
I get problems when I want to compare results from other analysis tools that keep the original names.
Likewise, an X is added to feature names that start with a number (e.g. ASV identifiers from QIIME 2).
The latter problem I can easily fix with regex, but the first mentioned problem is more difficult. Patterns that are predictable I can fix provided I know the characters that change to periods. However, since I can’t predict when there is a parenthesis or square bracket, I can’t correct the names.
Examples of predictable patterns (e.g. ;p__) and unpredicable patterns:
Contain square bracket:
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.7 (Ootpa)