relab_phyloseq {FAVA} | R Documentation |
Generate a relative abundance matrix with sample metadata and OTU abundances from a phyloseq object.
Description
The R package phyloseq streamlines the storage and analysis of microbiome sequence data. This function takes a phyloseq object and extracts the OTU table and the sample metadata and combines them into one relative abundance matrix with rows corresponding to samples, metadata on the left-hand side, and OTU relative abundances on the right-hand side.
Usage
relab_phyloseq(phyloseq_object)
Arguments
phyloseq_object |
A phyloseq object containing both an OTU table ( |
Value
A data frame with rows representing samples and columns representing sample data categories or OTU relative abundances. OTU abundances are automatically normalized so that they sum to 1 for each sample, though a warning will be provided if a renormalization was necessary.
Examples
if (requireNamespace("phyloseq", quietly = TRUE)) {
data(GlobalPatterns, package = "phyloseq")
# Make a small phyloseq object for demonstration
phyloseq_subset = phyloseq::subset_taxa(phyloseq::subset_samples(GlobalPatterns,
X.SampleID %in%
c("CL3", "CC1")),
Order == "Cenarchaeales")
otu_table = relab_phyloseq(phyloseq_subset)
otu_table[, 1:10]
}
[Package FAVA version 1.0.9 Index]