merge_taxa-methods: Merge a subset of the species in 'x' into one...

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

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.

See Also

tip_glom, tax_glom, merge_phyloseq, merge_samples

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")

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