README.md

In thomasp85/MSGFgui-release: A shiny GUI for MSGFplus

MSGFgui

This is an R package that functions as a GUI overlay for the MSGFplus package. Besides giving the user a visual way of running MS-GF+, it also present a large and engaging set of functions to evaluate the search results. The GUI is build using shiny and D3.js and thus requires a modern browser (which everyone should use anyway).

Main features

• Simpel and engaging GUI for running and evaluating MS/MS data using the MS-GF+ algorithm
• Statistical plots to evaluate a sample or a set of samples
• Dive into the identification data graphically, from protein, through peptide down to individual spectra
• Rich filtering options. Quickly get what you want by filtering on either the identification quality, the raw MS data or the search database data
• Access the data from another R session to continue your analysis directly within R
• Import already analysed data for comparison

Installation

MSGFgui and it's sister package MSGFplus is intented for inclusion within the next Bioconductor release. Until then, try it out by installing as follows:

source("http://bioconductor.org/biocLite.R")
biocLite('mzR')
biocLite('mzID')
install.packages('shiny')
install.packages('devtools')
library(devtools)
install_github('shinyFiles', 'thomasp85')
install_github('MSGFplus', 'thomasp85')
install_github('MSGFgui', 'thomasp85')

Usage

After installation the GUI can be launched from R by:

library(MSGFgui)
MSGFgui()

By launching a second R session while the GUI is running, the current identification data in the GUI can be accessed in R by:

library(MSGFgui)
data <- currentData()

The communication is one-way one-time though - modifications and deletion in the data from the second R session is not propagated to the GUI and if new data is added in the GUI the currentData() call has to be repeated for this to be visible in R.

Screenshots

Sample overview Protein view  Peptide view  Scan view  Filtering Tooltips Settings

Credit

Sangtae Kim is the developer behind the MS-GF+ algoritm, without which this package would be rather shallow. Furthermore he has provided fast and helpful feedback during the development process.

References

1. MSGFplus (R package)
2. MS-GF+ (Original Java program)

thomasp85/MSGFgui-release documentation built on May 31, 2019, 11:09 a.m.