The modified Screening and Ranking algorithm (modSaRa) can detect chromosome copy number variants with high sensitivity and specificity. For a sequence of intensity values, the modified SaRa will process it by quantile normalization, search for change-point candidates, eliminate unlikely change-points, and then output the potential CNV segments by presenting the start point and end point by SNP or CNV marker index.
To obtain and run modSaRa (Windows or Linux based), please download the source package with the file name extension “.tar.gz” and save it as "modSaRa_1.0.tar.gz." The source package needs to be compiled first with the Rtools on Windows and the Xcode on Mac. Please follow the following steps in R:
1. In R, Enter the directory where .tar.gz package file is saved,
2. Type the R command: install.packages("modSaRa_1.0.tar.gz",repos=NULL, type="source"),
3. Type the R command: library(modSaRa).
For Mac, users need to have Xcode installed on the computer before installing modSaRa. To that end, the following steps are also recommended for installing the .tar.gz file.
1. Go to http://hpc.sourceforge.net
2. Download the newest version of gcc-x.x-bin.tar.gz
3. Run “gunzip gcc-x.x-bin.tar.gz” in the Mac terminal (change the directory to where this package was saved first)
4. Run “sudo tar -xvf gcc-x.x-bin.tar -C /” in the Mac terminal
5. Run “install.packages(path_to_file, repos = NULL, type="source”)” in the Console window of RStudio or R, where path_to_file represents the full path and file name
Details of how to use the package for CNV analysis can be found in the Reference Manual.