README.md

In leeshawn/SKAT: SNP-Set (Sequence) Kernel Association Test

SKAT R-package

SKAT is an R-package for gene/region-based multiple variant tests. It has functions for Burden test, SKAT, and SKAT-O with adjusting for covariates and kinship.

Main Functions and key references

Following are main functions and key references. For details, please refer the package manual and vignettes.

1. SKAT function: Burden test, SKAT, and SKAT-O

   • Lee, S., Emond, M.J., ..., and Lin, X. (2012). Optimal unified approach for rare variant association testing with application to small sample case-control whole-exome sequencing studies. AJHG, 91, 224-237.
   • Lee, S., Wu, M. and Lin, X. (2012). Optimal tests for rare variant effects in sequencing association studies. Biostatistics, 13, 762-775
   • Wu, M., Lee, S., Cai, T., Li, Y., Boehnke, M. and Lin, X. (2011). Rare Variant Association Testing for Sequencing Data Using the Sequence Kernel Association Test (SKAT). AJHG, 89, 82-93.

2. Robust approaches functions for binary traits: SKATBinary_Robust and SKAT_CommonRare_Robust

3. Zhao, Z., Bi, W., Zhou, W., VanderHaar, P., Fritsche, L.G., Lee, S. (2020) UK Biobank Whole-Exome Sequence Binary Phenome Analysis with Robust Region-based Rare-Variant Test. AJHG, 2020, 3-12.

4. SKATBinary function: Burden test, SKAT, and SKAT-O with efficient resampling for binary traits

   • Lee, S., Fuchsberger, C., Kim, S., Scott, L. (2016) An efficient resampling method for calibrating single and gene-based rare variant association analysis in case-control studies, Biostatistics, 17, 1-15.

5. SKAT_CommonRare function: joint test for common and rare variants

   • Ionita-Laza, I., Lee, S., Makarov, V., Buxbaum, J. Lin, X. (2013). Sequence kernel association tests for the combined effect of rare and common variants. AJHG, 92, 841-853.

6. SKAT_ChrX function: X-chromosome test

   • Ma, C., Boehnke, M., Lee, S. and the GoT2D investigators (2015) Evaluating the calibration and power of three gene-based association tests for the X chromosome, Genetic Epidemiology, 39, 499-508.

7. SKAT_NULL_emmaX function: Kinship adjustment

8. SSD functions: plink binary file related functions

9. Power_Continuous, ...: power calculation functions

Link

• SKAT CRAN: Link
• SKAT google group: Link
• Example dataset: Link

leeshawn/SKAT documentation built on Feb. 5, 2023, 12:22 p.m.