panev.exprdataPreparation: PANEV gene expression dataset preparation

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

PANEV gene expression dataset preparation

Description

In case of an expression dataset, to run panev.exprnetwork function, PANEV requires a dataframe containing five columns labelled as follows: ensembl gene id, entrezgene, external gene name, FC, pvalue. This function helps to create a properly formatted dataframe, converting the gene list from ensembl or entrez gene annotation (or vice versa) and adding the gene symbol.

Usage

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

Arguments

in.file	Name of input file (with extension). The input file is a table with three columns labelled ensembl_gene_id OR 'entrezgene', 'FC' and 'pvalue', respectivelly. The input file must rely in the working directory.
gene_id	Type of annotation of provided gene list. You can choose among ensembl or entrez gene ID annotation (default = NULL).
biomart.species	The biomaRt species code of interest. You can check the list of all available species on biomaRt with the function panev.biomartSpecies (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 with five columns labeled 'ensembl_gene_id', 'entrezgene' and 'external_gene_name', 'FC', 'pvalue', 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 = "pig")
biomart.species <- as.character(list[6,1]) # sscrofa_gene_ensembl

#Convert the gene list with ensembl gene id
# Copy the example data file 'gene_list.txt' in the current working directory
genelist_converted <- panev.exprdataPreparation(in.file = "ensembl_expr_genelist.txt", 
                                              gene_id="ensembl", 
                                              biomart.species = biomart.species)

#Convert the gene list with entrez gene id
# Copy the example data file 'gene_list.txt' in the current working directory
genelist_converted <- panev.exprdataPreparation(in.file = "entrez_expr_genelist.txt", 
                                              gene_id="entrez", 
                                              biomart.species = biomart.species)

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