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.

Install the latest version of this package by entering the following in R:
install.packages("SKAT")
AuthorSeunggeun (Shawn) Lee, with contributions from Larisa Miropolsky and Michael Wu
Date of publication2016-06-28 20:16:35
MaintainerSeunggeun (Shawn) Lee <leeshawn@umich.edu>
LicenseGPL (>= 2)
Version1.2.1

View on CRAN

Functions

Files

inst
inst/doc
inst/doc/SKAT.pdf
inst/doc/SKAT.R
inst/doc/SKAT.Rnw
src
src/Binary_resampling.c
src/setid_bim_index.cpp
src/Binary_ComputeExact.h
src/Binary_ComputeExactSKATO.cpp
src/bed_reader.cpp
src/Binary_ComputeExact.cpp
src/DArray.h
src/mwo_reader.h
src/error_messages.h
src/Binary_global.h
src/Binary_ComputeExactMC.cpp
src/setid_bim_index.h
src/Binary_ComputeExactMC.h
src/bed_reader.h
src/mwo_reader.cpp
src/Binary_Permu_SKAT.cpp
src/NPsort.h
src/Binary_Permu_SKAT.h
src/Binary_HyperGeo.h
src/interface_to_R.cpp
src/kernel_func.c
src/Binary_global.cpp
src/interface.cpp
src/qfc.cpp
src/Binary_HyperGeo.cpp
src/interface_to_R.h
NAMESPACE
data
data/SKAT.example.rda
data/SKAT.fam.example.rda
data/SKAT.example.ChrX.rda
data/SKAT.haplotypes.rda
data/datalist
data/SKATBinary.example.rda
R
R/SKAT_Linear.R R/Power.R R/SKAT_EMMAX.R R/Joint_CommonRare.R R/X_Chrom.R R/Function_Power_Resampling.R R/SKAT_Optimal_VarMatching.R R/SKAT_CompQuadForm.R R/Binary_Result_Calibration.R R/MAIN.R R/MK_SSD_All_Output.R R/Binary_MAIN_ExactBin.R R/Main_SSD.R R/Null_Model.R R/SKAT_Logistic_VarMatching.R R/Binary_MAIN.R R/Kernel.R R/SSD.R R/Power_Corr.R R/Binary_single.b.firth.R R/Binary_Function1.R R/Binary_Etc.R R/Function.R R/SKAT_Logistic.R R/Binary_Function.R R/SKAT_Optimal.R
vignettes
vignettes/SKATBinary.example.bim
vignettes/Example1_Weight.txt
vignettes/Example1.bim
vignettes/Example1.Cov
vignettes/Example1.SetID
vignettes/Example1_old.fam
vignettes/Example1.fam
vignettes/Example1.zip
vignettes/SKATBinary.example.bed
vignettes/SKATBinary.example.cov
vignettes/SKATBinary.example.fam
vignettes/Example1.bed
vignettes/Example1_Ord.Cov
vignettes/SKATBinary.example.SetID
vignettes/Example1_NoHeader.Cov
vignettes/SKAT.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/SKAT.rd
man/Get_Genotypes_SSD.rd
man/Get_RequiredSampleSize.rd
man/SKAT.example.rd
man/Open_SSD.rd
man/Resampling_FWER.rd
man/SSD_FILE_OPEN.rd
man/Read_SNP_WeightFile.rd
man/SKAT_Null_Model_MomentAdjust.rd
man/SKATBinary_Single.rd
man/Read_Plink_FAM.rd
man/SKATBinary.rd
man/Get_Resampling_Pvalue.rd
man/SKAT.fam.example.rd
man/Close_SSD.rd
man/Get_ENT.rd
man/SKATBinary.example.rd
man/SKAT.haplotypes.rd
man/SKAT_Null_Model.rd
man/Power_Continuous.rd
man/QQPlot_Adj.rd
man/SKAT.SSD.All.rd
man/Generate_SSD_SetID.rd
man/Power_Logistic.rd
man/SKAT_CommonRare.rd
man/SKAT_ChrX.rd
man/SKAT_NULL_emmaX.rd
man/Get_Logistic_Weights.rd
man/SKAT.example.ChrX.rd
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