search

grunwaldlab / metacoder

Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
http://grunwaldlab.github.io/metacoder_documentation
Other
135 stars 28 forks source link

filter_taxa collides with command in phyloseq package #170

Open dougwyu opened 7 years ago

dougwyu commented 7 years ago

fyi. the phyloseq package also has a filter_taxa() command, so when I tried run the vignette, i got an error. After searching help on filter_taxa, i realised that i just needed to use metabarcoder::filter_taxa.

might be worth editing this in your vignette.

lovely package!

zachary-foster commented 7 years ago

Thanks for the report!

fyi. the phyloseq package also has a filter_taxa() command, so when I tried run the vignette, i got an error. After searching help on filter_taxa, i realised that i just needed to use metabarcoder::filter_taxa.

Yea, I noticed that recently too. I have not decided whether or not to change the name. Sorry about the error, I will look into that.

might be worth editing this in your vignette.

Yes, I will do that

lovely package!

Thanks!

FYI, the filter_taxa command, as well as all other manipulation functions and the taxmap class are being moved to the taxa package. The taxmap class has been improved there too. The next version of metacoder, will not have those, but instead depend on taxa.