gpdata {geneplast} | R Documentation

## A pre-processed dataset for the geneplast package.

### Description

A dataset used to demonstrate geneplast main functions.

### Usage

    data(gpdata.gs)

### Format

`gpdata.gs` data frame containing information about clusters of orthologous groups.

### Details

The dataset consists of 4 R objects used in the geneplast vignettes.

cogdata

  A data frame with three columns containing the Clusters of Orthologous Groups information retrieved from the STRING database (http://string-db.org/), release 9.1. Column 1 = Ensembl protein ID; column 2 = NCBI species ID;column 3 = OG ID.

sspids

  A data frame containing the species listed in STRING database (http://string-db.org/), release 9.1. Column 1 = NCBI species ID; column 2 = NCBI species name;column 3 = species domain (eukaryotes).

cogids

  A one-column data.frame with orthologous groups IDs available in the 'cogdata' object.

phyloTree

  An object of class "phylo" listing the eukaryotes in the STRING database, release 9.1.

### Value

a dataset.

### References

Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 2013 Jan;41(Database issue):D808-15. doi: 10.1093/nar/gks1094. Epub 2012 Nov 29.

### Examples

      data(gpdata.gs)

[Package geneplast version 1.20.1 Index]