panev.biomartSpecies: Gene list preparation species codes

In vpalombo/PANEV: PaNeV: an R package for a pathway-based network visualization

Gene list preparation species codes

Description

The function retrieves the correct organism code from ensembl.org website. This code is mandatory to run panev.dataPreparation and panev.exprdataPreparation, useful to generate a properly formatted gene list for PANEV, switching up-to-date gene identifiers from ensembl to entrez annotation (or vice versa).

Usage

panev.biomartSpecies(string = NULL)

Arguments

string

A string used to search the organism code within the full list. If NULL, a list with all available organisms is returned (default = NULL).

Details

This function is based on listDatasets function from biomaRt package (http://bioconductor.org/packages/release/bioc/html/biomaRt.html).

Value

A dataframe with the list of organisms available for gene list preparation. The dataframe contains three columns with organism_code, description and version respectively.

Author(s)

Valentino Palombo ([e-mail])

References

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Steffen Durinck, Paul T. Spellman, Ewan Birney and Wolfgang Huber, Nature Protocols 4, 1184-1191 (2009).

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Steffen Durinck, Yves Moreau, Arek Kasprzyk, Sean Davis, Bart De Moor, Alvis Brazma and Wolfgang Huber, Bioinformatics 21, 3439-3440 (2005).

Examples

##### EXAMPLES CODE #####
#Create a list of all available organisms
list <- panev.biomartSpecies(string = NULL)

#Look for a specific organism matching a search string 
list <- panev.biomartSpecies(string = "cow")

vpalombo/PANEV documentation built on June 13, 2022, 1:11 p.m.