sp_taxa_ID: Species ID taxonomoc classification

In SarahAsbury/retainresolve: Retain Resolve Microbiome Agglomeration

Species ID taxonomoc classification

Description

Add full taxonomic classification to species ID auto-generated by Phyloseq

Usage

sp_taxa_ID(physeq, taxa.col = NA, remove = FALSE, remove.delimiter = "_")

Arguments

physeq	Phyloseq object
taxa.col	String of taxonomic levels to include in classification. Taxonomic levels must exist in the input phyloseq object. If no input given, defaults to all levels in phyloseq object.
remove	TRUE or FALSE. Are there characters that need to be removed after the spID in the taxa rowname to isolate the spID ? If TRUE, spID is extracted (e.g sp1_bacteria_bacteroidetes extracted to sp1)
remove.delimiter	Character string that separates sp ID from remaining OTU name characters (e.g sp1_bacteria_bacteroidetes delimiter is "_")

Value

Returns the phyloseq object with taxonomic classification as part of the taxa name (i.e. phyloseq OTU table rownames now contain taxonomy).

Examples

sp_taxa_ID(dat) #Add full taxonomic label to rownames (i.e. sp###_Kingdom_Phylum_Class_Order_Family_Genus)
sp_taxa_ID(physeq = dat, taxa.col = c("Family, "Genus)) #Add full taxonomic label to rownames (i.e. sp###_Family_Genus)

SarahAsbury/retainresolve documentation built on Feb. 20, 2023, 7:48 a.m.