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SKAT (version 1.3.2)

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.

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Version

Install

install.packages('SKAT')

Monthly Downloads

1,382

Version

1.3.2

License

GPL (>= 2)

Maintainer

Seunggeun Shawn Lee

Last Published

July 24th, 2017

Functions in SKAT (1.3.2)

Get_Resampling_Pvalue

Compute a resampling p-value
Open_SSD

Open SNP set data file (SSD)
Get_EffectiveNumberTest

Estimate the effective number of tests for Bonferroni correction
Get_Genotypes_SSD

Get Genotype data from SSD file
Close_SSD

Close SNP set data file (SSD)
Generate_SSD_SetID

Generate SNP set data file (SSD)
Get_Logistic_Weights

Get the logistic weight
Get_RequiredSampleSize

Get the required sample size to achieve the given power
Power_Continuous

Power calculation, continuous traits
Power_Logistic

Power calculation, Dichotomous traits
SKAT

SNP-set (Sequence) Kernel Association Test
SKAT.SSD.All

SNP-set Kernel Association Test
SKATBinary

SNP set test for binary traits with asymptotic and efficient resampling methods
SKATBinary.example

Example data for SKAT
SKAT.fam.example

Example data for SKAT_NULL_emmaX
SKAT.haplotypes

Haplotype dataset for power calculation
SKAT_Null_Model

Get parameters and residuals from the NULL model
SKAT_Null_Model_MomentAdjust

Get parameters and residuals from the NULL model for small sample adjustment
Read_SNP_WeightFile

Read a file with custom weights
Resampling_FWER

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

Internal variables for SSD
SKAT.example.ChrX

Example data for SKAT
SKAT.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 chromosome variables
QQPlot_Adj

Adjusted QQ plot
Read_Plink_FAM

Read Plink FAM and covariates files
SKAT_CommonRare

SKAT for the combined effect of common and rare variants
SKAT_NULL_emmaX

Get parameters and residuals from the null model with incorporating the kinship structure