Package: SKAT 2.3.2

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_2.3.2.tar.gz
SKAT_2.3.2.zip(r-4.7)SKAT_2.3.2.zip(r-4.6)SKAT_2.3.2.zip(r-4.5)
SKAT_2.3.2.tgz(r-4.6-x86_64)SKAT_2.3.2.tgz(r-4.6-arm64)SKAT_2.3.2.tgz(r-4.5-x86_64)SKAT_2.3.2.tgz(r-4.5-arm64)
SKAT_2.3.2.tar.gz(r-4.7-arm64)SKAT_2.3.2.tar.gz(r-4.7-x86_64)SKAT_2.3.2.tar.gz(r-4.6-arm64)SKAT_2.3.2.tar.gz(r-4.6-x86_64)
SKAT_2.3.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SKAT/json (API)

# Install 'SKAT' in R:

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

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

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

SKAT.example - Example data for SKAT
SKAT.example.ChrX - Example data for SKAT
SKAT.fam.example - Example data for SKAT_NULL_emmaX
SKAT.haplotypes - Haplotype dataset for power calculation
SKATBinary.example - Example data for SKAT

On CRAN:

sequence cpp

10.05 score 54 stars 15 packages 412 scripts 1.1k downloads 407 mentions 56 exports 6 dependencies

Last updated from:0af21aa712. Checks:11 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	WARNING	167
linux-devel-x86_64	WARNING	177
source / vignettes	OK	207
linux-release-arm64	WARNING	159
linux-release-x86_64	WARNING	161
macos-release-arm64	WARNING	213
macos-release-x86_64	WARNING	588
macos-oldrel-arm64	WARNING	233
macos-oldrel-x86_64	WARNING	522
windows-devel	WARNING	169
windows-release	WARNING	144
windows-oldrel	WARNING	157
wasm-release	OK	134

Exports:Close_SSD Generate_SSD_SetID Get_Davies_PVal Get_EffectiveNumberTest Get_Genotypes_SSD Get_Genotypes_SSD_Sparse Get_Lambda Get_Liu_PVal Get_Logistic_Weights Get_Logistic_Weights_MAF Get_RequiredSampleSize Get_Resampling_Pvalue Get_Resampling_Pvalue_1 Open_SSD Power_Continuous Power_Continuous_R Power_Logistic Power_Logistic_R QQPlot_Adj Read_Plink_FAM Read_Plink_FAM_Cov Read_SNP_WeightFile Resampling_FWER Resampling_FWER_1 SKAT SKAT_Check_Method SKAT_ChrX SKAT_ChrY SKAT_CommonRare SKAT_CommonRare_Robust SKAT_CommonRare_Robust.SSD.All SKAT_CommonRare_Robust.SSD.OneSet SKAT_CommonRare_Robust.SSD.OneSet_SetIndex SKAT_CommonRare.SSD.All SKAT_CommonRare.SSD.OneSet SKAT_CommonRare.SSD.OneSet_SetIndex SKAT_META_Optimal SKAT_NULL_emmaX SKAT_Null_Model SKAT_Null_Model_ChrX SKAT_Null_Model_MomentAdjust SKAT_Optimal_Each_Q SKAT_Optimal_PValue_Davies SKAT_Optimal_PValue_Liu SKAT.SSD.All SKAT.SSD.OneSet SKAT.SSD.OneSet_SetIndex SKATBinary SKATBinary_Robust SKATBinary_Robust.SSD.All SKATBinary_Robust.SSD.OneSet SKATBinary_Robust.SSD.OneSet_SetIndex SKATBinary_Single SKATBinary.SSD.All SKATBinary.SSD.OneSet SKATBinary.SSD.OneSet_SetIndex

Dependencies:lattice Matrix Rcpp RcppEigen RSpectra SPAtest

SKAT

Rendered fromSKAT.Rnwusingutils::Sweave

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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 correction	Get_EffectiveNumberTest
Get Genotype data from SSD file	Get_Genotypes_SSD Get_Genotypes_SSD_Sparse
Get the logistic weight	Get_Logistic_Weights Get_Logistic_Weights_MAF
Get the required sample size to achieve the given power	Get_RequiredSampleSize
Compute a resampling p-value	Get_Resampling_Pvalue Get_Resampling_Pvalue_1
Open SNP set data file (SSD)	Open_SSD
Power calculation, continuous traits	Power_Continuous Power_Continuous_R
Power calculation, Dichotomous traits	Power_Logistic Power_Logistic_R
Adjusted QQ plot	QQPlot_Adj
Read Plink FAM and covariates files	Read_Plink_FAM Read_Plink_FAM_Cov
Read a file with custom weights	Read_SNP_WeightFile
Obtain significant SNP sets after controlling family wise error rate (FWER)	Resampling_FWER Resampling_FWER_1
SNP-set (Sequence) Kernel Association Test	SKAT SKAT.SSD.OneSet SKAT.SSD.OneSet_SetIndex
SNP-set (Sequence) Kernel Association Test for X and Y chromosome variables	SKAT_ChrX SKAT_ChrY
SKAT for the combined effect of common and rare variants	SKAT_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 methods	SKAT_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 structure	SKAT_NULL_emmaX
Get parameters and residuals from the NULL model	SKAT_Null_Model SKAT_Null_Model_ChrX
Get parameters and residuals from the NULL model for small sample adjustment	SKAT_Null_Model_MomentAdjust
Example data for SKAT	SKAT.example
Example data for SKAT	SKAT.example.ChrX
Example data for SKAT_NULL_emmaX	SKAT.fam.example
Haplotype dataset for power calculation	SKAT.haplotypes
SNP-set Kernel Association Test	SKAT.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 methods	SKATBinary SKATBinary.SSD.OneSet SKATBinary.SSD.OneSet_SetIndex
SNP set test for binary traits with robust region-based methods	SKATBinary_Robust SKATBinary_Robust.SSD.OneSet SKATBinary_Robust.SSD.OneSet_SetIndex
Single variant tests for binary traits with Firth and efficient resampling methods	SKATBinary_Single
Example data for SKAT	SKATBinary.example
Internal variables for SSD and functions for other packages	Get_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