PloGO2_R_Package

This project contains the package tar tar file, manual and vignette for the R package PloGO2, which helps with gene ontology and pathway analysis for multi-condition experiments. The package has been submitted to Bioconductor and is currently under review.

Dependencies

R version > 4.0

Installation

First install dependencies

install.packages(c('httr', 'openxlsx', 'xtable','heatmap3'))

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("GOstats")

BiocManager::install("GO.db")

BiocManager::install("clusterProfiler")

Next install PloGO2

From within R install from zipfile, using the file PloGO2_1.3.1.tar.gz

Testing

The example script for testing can be found in the script package folder

source(file.path(system.file("script", package="PloGO2"), "plogo2_script.R"))

Optional - use with the WGCNA workflow

BiocManager::install("impute")

BiocManager::install("preprocessCore")

install.packages('WGCNA')

Test the WGCNA workflow

source(file.path(system.file("script", package="PloGO2"), "WGCNA_proteomics.R"))

Example data

Three datasets in our paper are included in the example data folder.

Pathway database

KEGG pathway databases are available in the pathway DB folder for three common species: human, mouse and arabidopsis.