SKAT: SNP-Set (Sequence) Kernel Association Test

Functions for kernel-regression-based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently compute SNP-set level p-values. Methods available in this package include SKAT described in Micheal Wu, Seunggeun Lee et al. (2011) <doi:10.1016/j.ajhg.2011.05.029>, SKAT-O in Seunggeun Lee et al. (2012) <doi:10.1093/biostatistics/kxs014>, combined test of rare and common variants in Iuliana Ionita-Laza and Seunggeun Lee et al. (2013) <doi:10.1016/j.ajhg.2013.04.015>, efficient resampling for binary traits in Seunggeun Lee et al. (2016) <doi:10.1093/biostatistics/kxv033>, and robust test for binary traits in Zhangchen Zhao et al. (2020) <doi:10.1016/j.ajhg.2019.11.012>.

Version: 2.2.4
Depends: R (≥ 2.13.0), Matrix, SPAtest, RSpectra
Published: 2022-03-29
Author: Seunggeun (Shawn) Lee [aut, cre, cph], Zhangchen Zhao [aut], Larisa Miropolsky [aut], Michael Wu [aut]
Maintainer: Seunggeun (Shawn) Lee <lee7801 at snu.ac.kr>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
CRAN checks: SKAT results

Documentation:

Reference manual: SKAT.pdf
Vignettes: SKAT

Downloads:

Package source: SKAT_2.2.4.tar.gz
Windows binaries: r-devel: SKAT_2.2.4.zip, r-release: SKAT_2.2.4.zip, r-oldrel: SKAT_2.2.4.zip
macOS binaries: r-release (arm64): SKAT_2.2.4.tgz, r-release (x86_64): SKAT_2.2.4.tgz, r-oldrel: SKAT_2.2.4.tgz
Old sources: SKAT archive

Reverse dependencies:

Reverse depends: FSTpackage, GenoScan, LGEWIS, LGRF, Mega2R, WGScan
Reverse imports: GBJ, SMUT, zfa
Reverse suggests: BGData, bigQF, FastKM, seqminer

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