RAM (version 1.2.0)

core.OTU.rank: Summary Of Core OTUs

Description

This function returns a list showing otus that present in a pre-defined percent of samples in each level of a given metadata category.

Usage

core.OTU.rank(data, rank="g", drop.unclassified=TRUE,
                meta, meta.factor="", percent=1)

Arguments

data

a list of OTU tables to be analyzed. See also RAM.input.formatting.

rank

the taxonomic rank(s) of otu classification (see ?RAM.rank.formatting for formatting details).

drop.unclassified

logical, whether or not exclude unclassified groups.

meta

the metadata table to be analyzed.

meta.factor

the metadata qualitative variable

percent

the percent of samples in each level of the given metadata variable

Value

• core.OTU.rank returns a list containing otus that present in a pre-defined percent of samples in each level of a given metadata category. The outputs describe the following information for each level of a given metadata variable: 1) core otuID; 2) taxa the core otus assigned to; and 3) percent of core otus sequences vs. total sequences in each group. The last item in the list show the same information of otus that in all levels.

See Also

decostand

Examples

data(ITS1, meta)
core <- core.OTU.rank(data=list(ITS1=ITS1), rank="g", meta=meta, 
         meta.factor="City", percent=0.90)