Screen & Clean
Screen & Clean is a program that identifies associations between SNP allele count data and a continuous or binary phenotype. The core function is a screen that identifies the first K SNPs to enter an L1-penalized regression of the phenotype on the allele counts, where K is chosen by a stability criterion. The program includes several optional procedures that are turned off by default, including a pre-screen using marginal regression p-values, a second screen for pairwise interaction effects, and a multivariate regression clean of the screened SNPs. K may also be chosen directly by the user.
- Linux / Windows
- R Package
:: MORE INFORMATION
Wu, Devlin, Ringquist, Trucco, and Roeder
“Screen and Clean: A Tool for Identifying Interactions in Genome-Wide Association Studies”
Genet Epidemiol. 2010 April; 34(3): 275–285.