lowest_classified: Get the lowest classified ranks for the OTUs

In alexpiper/seqateurs: Tools for trimming and processing sequence data

Get the lowest classified ranks for the OTUs

Description

Get the lowest classified ranks for the OTUs

Usage

lowest_classified(x, sep = "__", return = "rank", rownames = TRUE)

Arguments

x	A matrix, data frame or phyloseq object
sep	The seperator between the rank, and the name i.e. G__Drosophila would be the default for an OTU that could only be assigned to the genus Drosophila
return	The type of values to return. Options include 'rank' which returns a character vector listing the lowest taxonomic each otu was classified to, i.e. Species, Genus etc 'taxon' returns a character vector listing the lowest taxonomic name each otu was classified to i.e. Drosophila_suzukii, Diptera etc 'both' returns a data frame containing both of the above
rownames	Whether rownames should be returned, or instead an OTU column

See Also

na_to_unclassified unclassified_to_na

alexpiper/seqateurs documentation built on July 9, 2023, 7:21 a.m.