phyloseq (version 1.16.2)

prune_samples: Define a subset of samples to keep in a phyloseq object.

Description

An S4 Generic method for pruning/filtering unwanted samples by defining those you want to keep.

Usage

prune_samples(samples, x)
## S3 method for class 'character,otu_table':
prune_samples(samples, x)
## S3 method for class 'character,sample_data':
prune_samples(samples, x)
## S3 method for class 'character,phyloseq':
prune_samples(samples, x)
## S3 method for class 'logical,ANY':
prune_samples(samples, x)

Arguments

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 samples is a named logical, the samples retained is based on those names. Make sure they are compatible with the sample_names of the object you are modifying (x).

x

A phyloseq object.

Value

• The class of the object returned by prune_samples matches the class of the phyloseq object, x.

See Also

subset_samples

Examples

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"))