Maaslin2 changes the feature names

Downstream analysis and statistics MaAsLin
1

Hi,

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.

Sincerely,
Jan

Examples of predictable patterns (e.g. ;p__) and unpredicable patterns:

Contain parenthesis:
d__Bacteria;p__Patescibacteria;c__Gracilibacteria;o__Absconditabacteriales_(SR1);f__Absconditabacteriales_(SR1);g__Absconditabacteriales_(SR1)

Contain square bracket:
d__Bacteria;p__Firmicutes;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__[Eubacterium]_hallii_group

Contain hyphen:
d__Bacteria;p__Firmicutes;c__Negativicutes;o__Veillonellales-Selenomonadales;f__Veillonellaceae;g__Veillonella

sessionInfo()
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)

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2

Hi @Jan

Unfortunately this is due to data frames in R not liking columns that start with numbers. Due to this base R automatically adds the character “X” infant of any columns that start with a number.

Similarly, R does not like the use of some punctuation in column names so they are replaced by “.”. My suggestion would be to replace all punctuation with “.” in your column names using regex and then doing the same for your original names to match between them.

cheers,
Jacob Nearing

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