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

In joey711/phyloseq: Handling and analysis of high-throughput microbiome census data

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)

## 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)

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"))

joey711/phyloseq documentation built on Nov. 4, 2022, 1:16 a.m.