Define a subset of samples to keep in a phyloseq object.
An S4 Generic method for pruning/filtering unwanted samples by defining those you want to keep.
prune_samples(samples, x) ## S4 method for signature 'character,otu_table' prune_samples(samples, x) ## S4 method for signature 'character,sample_data' prune_samples(samples, x) ## S4 method for signature 'character,phyloseq' prune_samples(samples, x) ## S4 method for signature 'logical,ANY' prune_samples(samples, x)
samples |
(Required). A character vector of the samples in object x that you want to
keep – OR alternatively – a logical vector where the kept samples are TRUE, and length
is equal to the number of samples in object x. If |
x |
A phyloseq object. |
The class of the object returned by prune_samples matches
the class of the phyloseq object, x.
data(GlobalPatterns) # Subset to just the Chlamydiae phylum. GP.chl <- subset_taxa(GlobalPatterns, Phylum=="Chlamydiae") # Remove the samples that have less than 20 total reads from Chlamydiae GP.chl <- prune_samples(sample_sums(GP.chl)>=20, GP.chl) # (p <- plot_tree(GP.chl, color="SampleType", shape="Family", label.tips="Genus", size="abundance"))
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