PerseusR

This repository contains the source code of the PerseusR software package. PerseusR contains convenience functions which allow for faster and easier development of plugins for Perseus in the R programming language. This page contains developer information on PerseusR, for high-level information please refer to the manuscript listed below.

PerseusR was designed to work in conjunction with the PluginInterop plugin, but can also be used stand-alone.

Citation

If you use PerseusR in your projects, please cite

Rudolph, J D and Cox, J 2018, A network module for the Perseus software for computational proteomics facilitates proteome interaction graph analysis doi:10.1101/447268

Installation

Make sure to have R >= 3.5.0 installed. Paste the following lines into an running R session. You can skip the comment lines starting with #.

install.packages(“BiocManager”)
BiocManager::install(“Biobase”)

# installing devtools first
install.packages("devtools")

# install PerseusR via devtools
library(devtools)
install_github("cox-labs/PerseusR")

Developing plugins

Perseus provides activities to call R scripts from within the workflow via PluginInterop, e.g. Matrix => R. Developing a plugin therefore translates to writing an R script that follows a small set of conventions. By adhering to these conventions, Perseus will be able to successfully communicate with R and transfer inputs and results between the programs. PerseusR provides the neccessary functions to make plugin development in R easy and straight forward.

This example R script adds 1 to all main columns in the matrix. While its functionality is very simple. It can serve as a starting point for more extensive scripts.

# All plugins can be split into 3 parts
# 1. Reading the command line arguments provided by Perseus and parsing the data.
# 2. Perform the desired functionality on the data.
# 3. Write the results to the expected locations in the Perseus formats.

# 1. Parse command line arguments passed in from Perseus,
# including input file and output file paths.
args = commandArgs(trailingOnly=TRUE)
if (length(args) != 2) {
	stop("Do not provide additional arguments!", call.=FALSE)
}
inFile <- args[1]
outFile <- args[2]


# Use PerseusR to read and write the data in Perseus text format.
library(PerseusR)
mdata <- read.perseus(inFile)

# The mdata object can be easily deconstructed into a number of different
# data frames. Check reference manual or help() for full list.
mainMatrix <- main(mdata)

# 2. Run any kind of analysis on the extracted data.
df <- mainMatrix + 1

# 3. Create a matrixData object which can be conveniently written to file
# in the Perseus txt format.
outMdata <- matrixData(main=df)
write.perseus(outMdata, outFile)

Licensing and contributions

PerseusR is licensed under the MIT license. Contributions are welcome.