Mass Spectrometry Research Center AIMS.2019 R package

This is the R package accompanying the AIMS R data analysis course, it will give uses a very brief introduction to the open-source Cardinal in R for basic data pre-processing and analysis tasks and includes some MSRC in-house developed functions for data analysis.

Installation

Please download and install R followed by RStudio.

1. Download and install latest version of R for your platform

2. Download and install latest version of RStudio Desktop for your platform

For MacOS users:

3. Download and install Xquartz for the imager depenency

Getting started for the first time

Open RStudio and run the following lines in the R Console to install the necessary packages:

##Cardinal must be installed before any other steps!!
if (!requireNamespace("BiocManager", quietly=TRUE))
  install.packages("BiocManager")

BiocManager::install("Cardinal")

##install R package devtools to install from github
install.packages('devtools')

##install the aimsMSRC package
require(devtools)
install_github('nhpatterson/aimsMSRC')

#load package
require(aimsMSRC)

What's next?

• Examine the tutorials:

  • Data reading and pre-processing to peaks, demo only, raw data not included due to size, R Markdown
  • Comparse two user selected ROIs using ROC analysis, R Markdown
  • Exploratory multivariate analysis, PCA and clustering, R Markdown
  • Export peak intensity tables into .csv, R Markdown
  • Convert & export data for data-driven image fusion, R Markdown