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.
Please download and install R followed by RStudio.
Open RStudio and run the following lines in the R Console to install the necessary packages:
##Cardinal must be installed before any other steps!!
source("http://bioconductor.org/biocLite.R")
biocLite("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)
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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