shared.OTU: Summary of Shared OTUs Across ALL Subjects

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

Description

This function consumes OTU tables and returns a list summarizing information about the presence of the OTUs in samples.

Usage

shared.OTU(data)

Arguments

data	a list of OTU tables to be analyzed.

Value

shared.OTU returns a list containing the information calculated. The names associated with the list describe what that number represents; i.e. "#_of_OTUs_in_all_samples" shows how many OTUs in the given table were found to be present in all samples. The last item in the list is a character vector, containing the OTU number and taxonomic information of each OTU which was present in all samples. All entries in that column are of the form "OTU-taxonomic_classification".

Note

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

Author(s)

Wen Chen and Joshua Simpson.

See Also

decostand

Examples

data(ITS1)
## Not run: 
shared <- shared.OTU(data=list(ITS1=ITS1))
shared <- shared.OTU(data=list(ITS1=ITS1, ITS2=ITS2))

## End(Not run)

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