SKAT Download

To use it, you need R >= 2.13.

Warnings: (for ver < 0.8) The previous versions have a bug in which it makes SKAT use incorrect MAFs to compute weights when binary plink files are used. SKAT assumes that genotypes are coded as the number of minor alleles, and computes MAFs based on it. For some plink files, SKAT gets genotypes as the number of major alleles, not minor alleles, which will severely underweight variants. Please reinstall the package if you use binary plink files.

 

User Group:
Please join in the SKAT/MetaSKAT Google Group to ask / discuss / comment about SKAT/MetaSKAT.

 

Download:
We uploaded the package to CRAN. You can download the package, manual, and vignettes from here.

You can install the SKAT R-package on MS Windows, UNIX/Linux, and Mac OSX. If you don’t know how to install an R-package, please see here.

SKAT-O:

To run SKAT-O, please set method=”optimal.adj” in the SKAT function, which provides a better type I error control in tail areas then method=”optimal”

Combined effect of common and rare variants:

From ver 0.9, you can use SKAT_CommonRare function to run a test for the combined effect of common and rare variants described in Ionita-Laza et al (-C and -A methods).

Changes:

Changes Ver 0.90: Add a SKAT_CommonRare function to carry out a test for the combined effect of common and rare variant.Ver 0.83: Add a function to read a plink covariate file (Read_Plink_FAM_Cov). To flip genotypes when they are coded as the number of major alleles.Ver 0.81: Fixed a bug related to binary plink files. Added method=”optimal.adj”Ver0.76: Fixed a bug related to IBS.weighted kernel.Ver 0.75: Uploaded to CRAN. Add a function to read FAM file.Ver 0.73: Sort snps and snpsets when sets are not contiguous.