panev.network: Pathways Network Visualization (PANEV)

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

Pathways Network Visualization (PANEV)

Description

The function performs a pathway analysis taking into account both upstream and downstream dependent network of functional related genes, from 2 to n degrees of interaction. This function generates n '.txt' files, one for each level of interaction, containing the candidate genes and the related pathways highlighted. Along with the tabular format results, the function gets also the diagram visualization of PANEV results, saved in an interactive '.html' file.

Usage

panev.network(in.file = NULL, out.file = "PANEV_gene", species = NULL, 
                  FL = NULL, levels = 2)

Arguments

in.file	Name of input file (with extension) containing the gene list of interest. The file must contain three columns labelled as 'ensembl_gene_id', 'entrezgene' and 'external_gene_name', respectively. The file must rely in the working directory. The handy function panev.dataPreparation could be used to create a properly formatted input file from a single gene list.
out.file	Name of the folder where the results will be stored and of the output diagram file (default = 'PANEV_gene').
species	The code of your species of interest. The correct code can get among the list of those available in KEGG with the handy function panev.speciesCode.
FL	A list of pathways of first level to investigate. The list of all available pathways can get with the panev.pathList function.
levels	The number of levels of interactions (from 1 to n) investingated (default = 2).

Details

For each level required for the investigation, a single .txt file will be generated, containing the genes and the related pathways for a specific level of interaction. The function get also the diagram visualization of results. This function is based on the main KEGGREST package (https://bioconductor.org/packages/release/bioc/html/KEGGREST.html).

Value

• The script generates from 1 to n 'txt' files, (with n equal to the levels of interaction required for the investigation). Each file is named (n)Lgenes, based on n level analysed and contains the genes falling inside the pathways of the specific degree of interaction investigated. Each file contains five columns with ensembl gene, entrez gene, gene name, path description and path id. The files are stored in a folder named as PANEV_RESULTS_<out.name>, created in the work directory.

• A <out.file>.html file with the diagram visualization of PANEV results. The file is stored in the same folder of .txt files

Author(s)

Valentino Palombo ([e-mail])

References

Tenenbaum D (2017). KEGGREST: Client-side REST access to KEGG. R package version 1.16.1.

Thieurmel B (2016). visNetwork: Network Visualization using 'vis.js' Library. R package version 2.0.3. https://CRAN.R-project.org/package=visNetwork

Examples

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

#Parameters
in.file="data.txt"
out.file="example"
FL = c("path:map00061", "path:map00062", "path:map00071", "path:map00072")
levels = 2

#Look for the specie code matching the search string 
list <- panev.speciesCode(string = "bos")
species=as.character(list[1,2]) # bta 

# Run the PANEV function
panev.network(in.file = in.file, 
              out.file = out.file, 
              species = species, 
              FL = FL, 
              levels = levels)
           

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