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SKAT (version 2.2.4)

SNP-Set (Sequence) Kernel Association Test

Description

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) , SKAT-O in Seunggeun Lee et al. (2012) , combined test of rare and common variants in Iuliana Ionita-Laza and Seunggeun Lee et al. (2013) , efficient resampling for binary traits in Seunggeun Lee et al. (2016) , and robust test for binary traits in Zhangchen Zhao et al. (2020) .

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Version

Install

install.packages('SKAT')

Monthly Downloads

21,684

Version

2.2.4

License

GPL (>= 2)

Maintainer

Seunggeun Lee

Last Published

March 29th, 2022

Functions in SKAT (2.2.4)

Power_Continuous

Power calculation, continuous traits
Open_SSD

Open SNP set data file (SSD)
Generate_SSD_SetID

Generate SNP set data file (SSD)
Get_RequiredSampleSize

Get the required sample size to achieve the given power
Get_Resampling_Pvalue

Compute a resampling p-value
Get_Logistic_Weights

Get the logistic weight
Get_EffectiveNumberTest

Estimate the effective number of tests for Bonferroni correction
Close_SSD

Close SNP set data file (SSD)
Power_Logistic

Power calculation, Dichotomous traits
Get_Genotypes_SSD

Get Genotype data from SSD file
QQPlot_Adj

Adjusted QQ plot
SKATBinary_Robust

SNP set test for binary traits with robust region-based methods
Resampling_FWER

Obtain significant SNP sets after controlling family wise error rate (FWER)
Read_SNP_WeightFile

Read a file with custom weights
SKAT_Null_Model

Get parameters and residuals from the NULL model
SKAT.haplotypes

Haplotype dataset for power calculation
SKAT.fam.example

Example data for SKAT_NULL_emmaX
SKAT_Null_Model_MomentAdjust

Get parameters and residuals from the NULL model for small sample adjustment
SKAT.example.ChrX

Example data for SKAT
SKAT.example

Example data for SKAT
SKATBinary.example

Example data for SKAT
SKATBinary_Single

Single variant tests for binary traits with Firth and efficient resampling methods
SKAT_ChrX

SNP-set (Sequence) Kernel Association Test for X and Y chromosome variables
Read_Plink_FAM

Read Plink FAM and covariates files
SKAT

SNP-set (Sequence) Kernel Association Test
SKAT_CommonRare

SKAT for the combined effect of common and rare variants
SKATBinary

SNP set test for binary traits with asymptotic and efficient resampling methods
SKAT_NULL_emmaX

Get parameters and residuals from the null model with incorporating the kinship structure
SKAT.SSD.All

SNP-set Kernel Association Test
SKAT_CommonRare_Robust

SNP set test (both common and rare variants) for binary traits with robust region-based methods
SSD_FILE_OPEN

Internal variables for SSD and functions for other packages