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 have a phyloseq object and I want to use the decontam packages for it to properly remove decontaminations from the "blank" samples (control), but when I do this:
sample_data(PS)$is.neg <- sample_data(PS)$Contaminant == "1"
then it all the sample information of the PS (phyloseq object).
Hey there,
I have a phyloseq object and I want to use the decontam packages for it to properly remove decontaminations from the "blank" samples (control), but when I do this: sample_data(PS)$is.neg <- sample_data(PS)$Contaminant == "1"
then it all the sample information of the PS (phyloseq object).