modSaRa — Modified Screening and Ranking Algorithm to Detect Chromosome Copy Number Variations

The modified Screening and Ranking algorithm 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.

To obtain and run modSaRa (Windows or Linux based), please download the zipped file for windows system and the gz file for linux system, and follow the following steps in R:

  • For Windows system,
    1. select "packages" on the top of R Gui, choose "install package from local zip file," and select the "modSaRa_1.0.zip" file.
    2. Type the R command: library(modSaRa).
  • For Linux system, 
    1. enter the directory where .tar.gz package file is saved and type "R", type R command: install.packages("modSaRa_1.0.tar.gz",repos=NULL,type="source"),
    2. Type the R command: library(modSaRa)