RAM (version 1.2.0)

valid.taxonomy: Validate And Reformat The OTU Taxonomy Column

Description

A properly formatted taxonomy column of an otu table is critical for RAM functions to run properly. The taxonomy column of an otu table is composed of taxonomic lineages for otuIDs. RAM accept 7 ranks, including kingdom, phylum, class, order, family, genus and species, sub ranks are not supported. Taxa names at each rank should have prefix as "k__", "p__", "c__", "o__", __", "g__", and "s__", each rank should be separated by "; ", i.e. a semi colon and a white space, NOT just ";".

This function will check the format of the taxonomy column of the input otu table and give suggetions that whether or not it needs to be reformatted using reformat.taxonomy of RAM.

However, RAM does accept missing ranks in lineages, as long as each rank is separated by "; " with proper prefix.

Usage

valid.taxonomy(data)
reformat.taxonomy(data, input.ranks, sep="; ")

Arguments

data

a list of otu tables, see RAM.input.formatting.

input.ranks

the ranks of the taxonomic lineages in the input otu tables.

sep

the separator between each taxonomic rank in the lineage.

See Also

get.rank, tax.abund

Examples

data(ITS1)
# for demonstration purpose only
# the ITS1 dataset missing species rank, but it's ok
# the problematic taxonomy lineages are those missing proper prefix 
# at each rank
# see ?RAM.rank.formatting
valid.taxonomy(data=list(ITS1=ITS1))
input.ranks <- c("kingdom", "phylum", "class", "order", "family", 
                  "genus")
reform.ITS1 <- reformat.taxonomy(list(ITS1=ITS1), 
                                 input.ranks=input.ranks,
                                 sep="; ")[[1]]