RAM (version 1.2.0)

get.rank: Get OTUs Classified at Taxonomic Rank(s)

Description

This function returns the OTUs of the given OTU table(s) which are classified at the given taxonomic rank.

Usage

get.rank(otu1, otu2 = NULL, rank = NULL)

Arguments

otu1

the first OTU table to be used.

otu2

the second OTU table to be used.

rank

a character vector representing a rank. Must be in one of three specific formats (see RAM.rank.formatting for help). If omitted, the function will repeat for all seven major taxonomic ranks.

Value

• The value returned by this function may become nested lists, so for convenience, any nested lists have been given descriptive items names to make accessing its elements simple (see Examples).
  • Ifotu2is given:
    • Ifrankis given: a list containing two data frames (otu1 and otu2 selected at the given rank).
    • Ifrankis not given: a list containing two lists. The first sublist representsotu1, the secondotu2. The sublists contain seven data frames, which are the OTU tables selected at each taxonomic rank (see Examples).
  • Ifotu2is not given:
    • Ifrankis given: a single data frame (otu1 selected at the given rank).
    • Ifrankis not given: a list containing seven data frames (otu1 selected at each taxonomic rank).

Examples

data(ITS1, ITS2)

    # the following are equivalent:
    ITS1.p <- get.rank(ITS1, rank="p")
    # this list has get.rank(ITS1, rank="k"),
    #               get.rank(ITS1, rank="p"), ...
    lst <- get.rank(ITS1) 
    stopifnot(identical(ITS1.p, lst$phylum)) 
    # true

    # get a list of length 2: the item holds all ITS1 data, the 
    # second holds ITS2 data
    lst.all <- get.rank(ITS1, ITS2)
    stopifnot(identical(ITS1.p, lst.all$otu1$phylum))