gpdata: A pre-processed dataset for the geneplast package.

In geneplast: Evolutionary and plasticity analysis of orthologous groups

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)

Example output

geneplast documentation built on Nov. 8, 2020, 7:57 p.m.