phyloseq: merge_taxa-methods – R documentation

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merge_taxa-methods

Merge a subset of the species in x into one species/taxa/OTU.

Description

Takes as input an object that describes species/taxa (e.g. phyloseq-class, otu_table-class, phylo-class, taxonomyTable-class), as well as a vector of species that should be merged. It is intended to be able to operate at a low-level such that related methods, such as tip_glom and tax_glom can both reliably call merge_taxa for their respective purposes.

Usage

merge_taxa(x, eqtaxa, archetype=1)

## S4 method for signature 'phyloseq'
merge_taxa(x, eqtaxa,
  archetype = eqtaxa[which.max(taxa_sums(x)[eqtaxa])])

## S4 method for signature 'sample_data'
merge_taxa(x, eqtaxa, archetype = 1L)

## S4 method for signature 'otu_table'
merge_taxa(x, eqtaxa,
  archetype = eqtaxa[which.max(taxa_sums(x)[eqtaxa])])

## S4 method for signature 'phylo'
merge_taxa(x, eqtaxa, archetype = 1L)

## S4 method for signature 'XStringSet'
merge_taxa(x, eqtaxa, archetype = 1L)

## S4 method for signature 'taxonomyTable'
merge_taxa(x, eqtaxa, archetype = 1L)

Arguments

`x`	(Required). An object that describes species (taxa). This includes `phyloseq-class`, `otu_table-class`, `taxonomyTable-class`, `phylo`.
`eqtaxa`	(Required). The species names, or indices, that should be merged together. If `length(eqtaxa) < 2`, then the object `x` will be returned safely unchanged.
`archetype`	(Optional). A single-length numeric or character. The index of `eqtaxa`, or OTU ID, indicating the species that should be kept to represent the summed/merged group of species/taxa/OTUs. The default is to use the OTU with the largest count total if counts are available, or to use `1` (the first OTU in `eqtaxa`) otherwise. If `archetype` is not a valid index or index-name in `eqtaxa`, the first will be used, and the value in archetype will be used as the index-name for the new species.

Value

The object, x, in its original class, but with the specified species merged into one entry in all relevant components.

Examples

#
data(esophagus)
tree <- phy_tree(esophagus)
otu  <- otu_table(esophagus)
otutree0 <- phyloseq(otu, tree)
# plot_tree(otutree0)
otutree1 <- merge_taxa(otutree0, 1:8, 2)
# plot_tree(esophagus, ladderize="left")

phyloseq

Handling and analysis of high-throughput microbiome census data

v1.34.0

AGPL-3

Authors

Paul J. McMurdie <joey711@gmail.com>, Susan Holmes <susan@stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain

Initial release

2019-04-23