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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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metagenomic data-filtering for bacteria and fungi #1138

Open oatesa opened 5 years ago

oatesa commented 5 years ago

I have metagenmoic data, i would like to analyse the bacteria and yeast (separately) removing kindgom e.g. viruses etc is there a way to filter these out?

mikemc commented 5 years ago

Hi @oatesa. The first step with a question like this is to take a look at the phyloseq tutorials and vignettes (run browseVignettes("phyloseq") inside R). In your case, keep an eye out for sections on filtering taxa. Typically the function you want to use for this purpose is the subset_taxa() function, which you can learn about by running ?subset_taxa or help(subset_taxa) in your R terminal