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:
I would like to find common otus in my phyloseq object with low coefficient of variation across sites (a specific threshold) and that are observed at least once in more than 2 sites. How can I do it I found this in the tutorial GPr = transform_sample_counts(mon, function(x) x/sum(x))
GP3f = filter_taxa(GPr, function(x) var(x) > 1e-05, TRUE) it should be something like this right?
thanks
I would like to find common otus in my phyloseq object with low coefficient of variation across sites (a specific threshold) and that are observed at least once in more than 2 sites. How can I do it I found this in the tutorial GPr = transform_sample_counts(mon, function(x) x/sum(x)) GP3f = filter_taxa(GPr, function(x) var(x) > 1e-05, TRUE) it should be something like this right? thanks