core.OTU.rank: Summary Of Core OTUs

In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

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.

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

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.