panev.dataPreparation: PANEV gene list preparation

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

PANEV gene list preparation

Description

The function helps to create a properly formatted gene list required by panev.network: a dataframe with three columns labelled as 'ensembl_gene_id', 'entrezgene' and 'external_gene_name', respectively.

Usage

panev.dataPreparation(in.file, gene_id = NULL, biomart.species = NULL)

Arguments

in.file	Name of input file (with extension). The input file is a one column list of genes of interest, in ensembl or entrez gene annotation. The file must rely in the working directory.
gene_id	Type of gene identifiers provided. User can choose among ensembl or entrez gene ID annotation (default = NULL).
biomart.species	The biomaRt organism code. The handy function panev.biomartSpecies is provided to retrieve the correct code (default = NULL).

Details

This function is based on the main biomaRt (http://bioconductor.org/packages/release/bioc/html/biomaRt.html) query function getBM which, given a set of filters and corresponding values, it retrieves the user specified attributes from the BioMart database one is connected to.

Value

A <in.file>_converted.txt file containing three columns with 'ensembl_gene_id', 'entrezgene' and 'external_gene_name' respectively, stored in the working directory.

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 #####
#Copy the example files in the current working directory
panev.example()

#Look for the organism code matching the search string 
list <- panev.biomartSpecies(string = "cow")
biomart.species <- as.character(list[1,1]) # btaurus_gene_ensembl

#Prepare PANEV input file using a gene list containing ensembl gene id.
genelist_converted <- panev.dataPreparation(in.file = "ensembl_genelist.txt", 
                                          gene_id = "ensembl", 
                                          biomart.species = biomart.species)

#Prepare PANEV input file using a gene list containing entraz gene id.
genelist_converted <- panev.dataPreparation(in.file = "entrez_genelist.txt", 
                                          gene_id = "entrez", 
                                          biomart.species = biomart.species)

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