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.

Author
Seunggeun (Shawn) Lee, with contributions from Larisa Miropolsky and Michael Wu
Date of publication
2016-06-28 20:16:35
Maintainer
Seunggeun (Shawn) Lee <leeshawn@umich.edu>
License
GPL (>= 2)
Version
1.2.1

View on CRAN

Files in this package

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