Taraoceans: TARA Oceans datasets

In LinkHD: LinkHD: a versatile framework to explore and integrate heterogeneous data

Description

TARA Oceans was an expedition allowing to the study of plankton communities and their interactions with enviromental variables. This dataset was taken from mixkernel package (https://cran.r-project.org/web/packages/mixKernel/index.html). Data constists on 139 prokaryotic-enriched samples collected from 68 stations and spread across threedepth layers: the surface (SRF), the deep chlorophyll maximum (DCM) layer and the mesopelagic(MES) zones. Samples were located in height different oceans or seas: Indian Ocean (IO), Mediter-ranean Sea (MS), North Atlantic Ocean (NAO), North Pacific Ocean (NPO), Red Sea (RS), SouthAtlantic Ocean (SAO), South Pacific Ocean (SPO) and South Ocean (SO).

Usage

data("Taraoceans")

Format

A list with seven components:

phychemdata

matrix with 139 rows and 22 columns. Each row represents a sample and each column an environmental variable.

pro.phylo

a matrix with 139 rows (samples) and 356 columns (prokaryotic OTUs).

taxonomy

a matrix with 356 rows (prokaryotic OTUs) and 6 columns indicating the taxonomy of each OTU.

phylogenetic.tree

a phylo object (see package <e2><80><99>ape<e2><80><99>) representing the prokaryotic OTUs

pro.NOGs

a matrix with 139 rows (samples) and 638 columns (NOGs).

GO

a list with the names of Gene Ontologies.

sample

a list containing three following entries (all three are character vectors):name(samplename),ocean(oceanic region of the sample) and depth(sample depth)

References

Sunagawa S., Coelho L.P., Chaffron S., Kultima J.R., Labadie K., Salazar F., Djahanschiri B., ZellerG., Mende D.R., Alberti A., Cornejo-Castillo F., Costea P.I., Cruaud C., d<e2><80><99>Oviedo F., Engelen S.,Ferrera I., Gasol J., Guidi L., Hildebrand F., Kokoszka F., Lepoivre C., Lima-Mendez G., PoulainJ., Poulos B., Royo-Llonch M., Sarmento H., Vieira-Silva S., Dimier C., Picheral M., Searson S.,Kandels-Lewis S.,TaraOceans coordinators, Bowler C., de Vargas C., Gorsky G., Grimsley N.,Hingamp P., Iudicone D., Jaillon O., Not F., Ogata H., Pesant S., Speich S., Stemmann L., SullivanM., Weissenbach J., Wincker P., Karsenti E., Raes J., Acinas S. and Bork P. (2015). Structure andfunction of the global ocean microbiome.Science,348, 6237

Examples

data(Taraoceans)

Example output

Loading required package: ggplot2

LinkHD documentation built on Nov. 8, 2020, 5:08 p.m.