panev.exprnetwork: PANEV on gene expression datasets

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

PANEV on gene expression datasets

Description

The function visualizes PANEV results from expression gene datasets, considering any interactions among selected pathways. For each pathway the diagram helps to visualize associated genes that overcome a user defined p-value threshold. The color is based on the fold change (FC) value.

Usage

panev.exprnetwork(in.file = NULL, path.file = NULL, out.file = "PANEV_expr", 
                      species = NULL, pvalue = 0.05)

Arguments

in.file	Name of input file (with extension). The input file containing the differentially expressed genes (DEG) analysis results. The file must contain five columns labeled 'ensembl_gene_id', 'entrezgene', 'external_gene_name', 'FC' and 'pvalue'. The panev.exprdataPreparation function can be used to create the properly formatted input file from a gene expression list. The input file must rely in working directory (default = NULL).
path.file	Name of input file (with extension). The input file containing two columns labeled path_ID and value, containing respectively the ID of pathways of interest (panev.pathList function could be used to check if they are available), and relative biological estimated score value (e.g. flux value obtained with Dinamic Impact Approach analysis developed and described by Bionaz et al., 2012). The input file must rely in working directory (default = NULL).
out.file	Name of output diagram file and folder where results will be stored (default = "PANEV_expr").
species	The KEGG organism code. The correct code for the species of interest can be retrieved with the handy panev.speciesCode function (default = NULL).
pvalue	The p-value cut-off for Differentially Expressed (DE) analysis (default = 0.05).

Details

This function is based on the main KEGGREST query function keggLink.

Value

A <out.file>.html file with the diagram visualization of PANEV results is created and stored in a folder named as PANEV_exprRESULTS_<out.name>, created in the work directory.

Author(s)

Valentino Palombo ([e-mail])

References

Bionaz, M., K. Periasamy, S.L. Rodriguez-Zas, W.L. Hurley, and J.J. Loor. 2012. A novel dynamic impact approach (DIA) for functional analysis of time-course omics studies: validation using the bovine mammary transcriptome. PLos One 7:e32455. doi:10.1371/journal.pone.0032455.

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 = "exprdata.txt"
path.file  = "expr_listPath.txt"
out.file = "expression_data"
pvalue = 0.05

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

# Run the PANEV function
panev.exprnetwork(in.file = in.file, 
                  path.file = path.file, 
                  out.file = out.file, 
                  species = species, 
                  pvalue = pvalue)

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