SKATplus: A Gene- or Pathway-Based Test of Association

Description Usage Arguments Details Value Author(s) References Examples

View source: R/SKATplus.R

Description

SKATlus provides enhanced power over SKAT by properly estimating the null distribution of SKAT.

Usage

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SKATplus(y, G, X=NULL, out_type="D", tau=NULL, permutation=FALSE, B=1000)

Arguments

y

a vector of phenotype on n subjects.

G

an n\times m matrix of SNP genotypes of n study subjects at m loci.

X

a matrix of covariates. It has n rows.

out_type

an indicator of the outcome type. "C" for the continuous outcome and "D" for the dichotomous outcome.

tau

proportion of selected subjects used for SKATplus.

permutation

an indicator. Use permutation for p-value or not.

B

the number of permutations if permutation=TRUE

Details

This version uses only subjects with lower phenotypic values for estimating the null distribution. That is, the "controls" are those of lower phenotypic values. When "controls" are of higher phenotypic values, change the sign of the phenotypic values in order to use this function.

Value

A list with class "htest" containing the following components:

statistic

the value of the test statistic, which is the same as SKAT statistic.

parameter

sample size and the number of SNPs

p.value

the p-value for SKATplus computed using Davies' method.

method

a character string indicting the test performed.

data.name

a character string giving the name of the data.

Author(s)

Kai Wang <kai-wang@uiowa.edu>

References

Wang, K. (2016) Boosting the power of the sequence kernel association test (SKAT) almost surely by properly estimating its null distribution. A J Hum Genet. In press.

Examples

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n=1000
y = c(rep(1, n/2), rep(0, n/2))
maf = seq(0.05, 0.5, 0.05)
g = NULL
for (j in 1:10){
        geno.freq = c(maf[j]^2, 2*maf[j]*(1-maf[j]), (1-maf[j])^2)
        g = cbind(g, sample(c(0,1,2), n, replace=TRUE, prob=geno.freq))
}
SKATplus(y, g, X=NULL, out_type="D", tau=NULL, permutation=FALSE, B=1000)

Example output

Loading required package: lattice
Loading required package: CompQuadForm

	SKAT+: gene- or pathway-based test of association based on a proper
	null

data:  g and y and NULL
SKAT = 771.5, #SNPs = 10, #subjects = 1000, % used for the null = 50,
p-value = 0.5561

iGasso documentation built on May 2, 2019, 4:20 a.m.