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Select a subset of taxa in a specified order where possible

Source: R/speedyseq_functions.R
select_taxa-methods.Rd

Select (a subset of) taxa; if x allows taxa to be reordered, then taxa are given in the specified order.

Usage

select_taxa(x, taxa, reorder = TRUE)

# S4 method for sample_data,character
select_taxa(x, taxa)

# S4 method for otu_table,character
select_taxa(x, taxa, reorder = TRUE)

# S4 method for taxonomyTable,character
select_taxa(x, taxa, reorder = TRUE)

# S4 method for XStringSet,character
select_taxa(x, taxa, reorder = TRUE)

# S4 method for phylo,character
select_taxa(x, taxa)

# S4 method for phyloseq,character
select_taxa(x, taxa, reorder = TRUE)

Arguments

x

A phyloseq object or phyloseq component object

taxa

Character vector of taxa to select, in requested order

reorder

Logical specifying whether to use the order in taxa (TRUE) or keep the order in taxa_names(x) (FALSE)

Details

This is a simple selector function that is like prune_taxa(taxa, x) when taxa is a character vector but always gives the taxa in the order taxa if possible (that is, except for phy_tree's and phyloseq objects that contain phy_tree's).

Author

Michael R. McLaren (orcid: 0000-0003-1575-473X)