Package: SKAT 2.2.5

Seunggeun (Shawn) Lee

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.

Authors:Seunggeun Lee and Zhangchen Zhao, with contributions from Larisa Miropolsky and Michael Wu

SKAT_2.2.5.tar.gz
SKAT_2.2.5.zip(r-4.5)SKAT_2.2.5.zip(r-4.4)SKAT_2.2.5.zip(r-4.3)
SKAT_2.2.5.tgz(r-4.4-x86_64)SKAT_2.2.5.tgz(r-4.4-arm64)SKAT_2.2.5.tgz(r-4.3-x86_64)SKAT_2.2.5.tgz(r-4.3-arm64)
SKAT_2.2.5.tar.gz(r-4.5-noble)SKAT_2.2.5.tar.gz(r-4.4-noble)
SKAT_2.2.5.tgz(r-4.4-emscripten)SKAT_2.2.5.tgz(r-4.3-emscripten)
SKAT.pdf |SKAT.html✨
SKAT/json (API)

# Install 'SKAT' in R:
install.packages('SKAT', repos = c('https://leelabsg.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/leelabsg/skat/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

sequence

55 exports 41 stars 6.74 score 6 dependencies 15 dependents 407 mentions 216 scripts 1.2k downloads

Last updated 2 years agofrom:7cac4d6cda. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 27 2024
R-4.5-win-x86_64WARNINGAug 27 2024
R-4.5-linux-x86_64WARNINGAug 27 2024
R-4.4-win-x86_64WARNINGAug 27 2024
R-4.4-mac-x86_64WARNINGAug 27 2024
R-4.4-mac-aarch64WARNINGAug 27 2024
R-4.3-win-x86_64WARNINGAug 27 2024
R-4.3-mac-x86_64WARNINGAug 27 2024
R-4.3-mac-aarch64WARNINGAug 27 2024

Exports:Close_SSDGenerate_SSD_SetIDGet_Davies_PValGet_EffectiveNumberTestGet_Genotypes_SSDGet_Genotypes_SSD_SparseGet_LambdaGet_Liu_PValGet_Logistic_WeightsGet_Logistic_Weights_MAFGet_RequiredSampleSizeGet_Resampling_PvalueGet_Resampling_Pvalue_1Open_SSDPower_ContinuousPower_Continuous_RPower_LogisticPower_Logistic_RQQPlot_AdjRead_Plink_FAMRead_Plink_FAM_CovRead_SNP_WeightFileResampling_FWERResampling_FWER_1SKATSKAT_Check_MethodSKAT_ChrXSKAT_ChrYSKAT_CommonRareSKAT_CommonRare_RobustSKAT_CommonRare_Robust.SSD.AllSKAT_CommonRare_Robust.SSD.OneSetSKAT_CommonRare_Robust.SSD.OneSet_SetIndexSKAT_CommonRare.SSD.AllSKAT_CommonRare.SSD.OneSetSKAT_CommonRare.SSD.OneSet_SetIndexSKAT_NULL_emmaXSKAT_Null_ModelSKAT_Null_Model_ChrXSKAT_Null_Model_MomentAdjustSKAT_Optimal_Each_QSKAT_Optimal_PValue_DaviesSKAT_Optimal_PValue_LiuSKAT.SSD.AllSKAT.SSD.OneSetSKAT.SSD.OneSet_SetIndexSKATBinarySKATBinary_RobustSKATBinary_Robust.SSD.AllSKATBinary_Robust.SSD.OneSetSKATBinary_Robust.SSD.OneSet_SetIndexSKATBinary_SingleSKATBinary.SSD.AllSKATBinary.SSD.OneSetSKATBinary.SSD.OneSet_SetIndex

Dependencies:latticeMatrixRcppRcppEigenRSpectraSPAtest

SKAT

Rendered fromSKAT.Rnwusingutils::Sweaveon Aug 27 2024.

Last update: 2020-12-23
Started: 2016-08-29

Readme and manuals

Help Manual

Help pageTopics
Close SNP set data file (SSD)Close_SSD
Generate SNP set data file (SSD)Generate_SSD_SetID
Estimate the effective number of tests for Bonferroni correctionGet_EffectiveNumberTest
Get Genotype data from SSD fileGet_Genotypes_SSD Get_Genotypes_SSD_Sparse
Get the logistic weightGet_Logistic_Weights Get_Logistic_Weights_MAF
Get the required sample size to achieve the given powerGet_RequiredSampleSize
Compute a resampling p-valueGet_Resampling_Pvalue Get_Resampling_Pvalue_1
Open SNP set data file (SSD)Open_SSD
Power calculation, continuous traitsPower_Continuous Power_Continuous_R
Power calculation, Dichotomous traitsPower_Logistic Power_Logistic_R
Adjusted QQ plotQQPlot_Adj
Read Plink FAM and covariates filesRead_Plink_FAM Read_Plink_FAM_Cov
Read a file with custom weightsRead_SNP_WeightFile
Obtain significant SNP sets after controlling family wise error rate (FWER)Resampling_FWER Resampling_FWER_1
SNP-set (Sequence) Kernel Association TestSKAT SKAT.SSD.OneSet SKAT.SSD.OneSet_SetIndex
SNP-set (Sequence) Kernel Association Test for X and Y chromosome variablesSKAT_ChrX SKAT_ChrY
SKAT for the combined effect of common and rare variantsSKAT_CommonRare SKAT_CommonRare.SSD.OneSet SKAT_CommonRare.SSD.OneSet_SetIndex
SNP set test (both common and rare variants) for binary traits with robust region-based methodsSKAT_CommonRare_Robust SKAT_CommonRare_Robust.SSD.OneSet SKAT_CommonRare_Robust.SSD.OneSet_SetIndex
Get parameters and residuals from the null model with incorporating the kinship structureSKAT_NULL_emmaX
Get parameters and residuals from the NULL modelSKAT_Null_Model SKAT_Null_Model_ChrX
Get parameters and residuals from the NULL model for small sample adjustmentSKAT_Null_Model_MomentAdjust
Example data for SKATSKAT.example
Example data for SKATSKAT.example.ChrX
Example data for SKAT_NULL_emmaXSKAT.fam.example
Haplotype dataset for power calculationSKAT.haplotypes
SNP-set Kernel Association TestSKAT.SSD.All SKATBinary.SSD.All SKATBinary_Robust.SSD.All SKAT_CommonRare.SSD.All SKAT_CommonRare_Robust.SSD.All
SNP set test for binary traits with asymptotic and efficient resampling methodsSKATBinary SKATBinary.SSD.OneSet SKATBinary.SSD.OneSet_SetIndex
SNP set test for binary traits with robust region-based methodsSKATBinary_Robust SKATBinary_Robust.SSD.OneSet SKATBinary_Robust.SSD.OneSet_SetIndex
Single variant tests for binary traits with Firth and efficient resampling methodsSKATBinary_Single
Example data for SKATSKATBinary.example
Internal variables for SSD and functions for other packagesGet_Davies_PVal Get_Lambda Get_Liu_PVal SKAT_Check_Method SKAT_Optimal_Each_Q SKAT_Optimal_PValue_Davies SKAT_Optimal_PValue_Liu SSD_FILE_OPEN.FileName SSD_FILE_OPEN.isOpen