core.OTU.rank: Summary Of Core OTUs

Description Usage Arguments Value Note Author(s) See Also Examples

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

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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.

Note

The taxon groups are determined to be absent/present using the "pa" method from the function decostand.

Author(s)

Wen Chen

See Also

decostand

Examples

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data(ITS1, meta)
## Not run: 
core <- core.OTU.rank(data=list(ITS1=ITS1), rank="g", meta=meta,
         meta.factor="City", percent=0.90)

## End(Not run)

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-4
Loading required package: ggplot2

RAM documentation built on May 2, 2019, 3:04 p.m.