iECAT_SingleVar: Integrating External Controls to Association Tests

In iECAT: Integrating External Controls into Association Test

Description

Test for association of a single variant with integrating external study samples to improve power

Usage

	iECAT_SingleVar(Z, obj, tbl.external, Fisher.test=FALSE, weight.factor=NULL)
	iECAT_SingleVar_Tbl(Tbl, Fisher.test=FALSE, weight.factor=NULL)
 

Arguments

Z	a numeric genotype vector for the variant. Each genotype should be coded as 0, 1, 2, and 9 (or NA) for AA, Aa, aa, and missing. A does not need to be a major allele.
obj	an output object of the SKAT_Null_Model function.
tbl.external	a vector of allele count from the external control.
Fisher.test	an indicator variable (default= "FALSE") to indicate whether to obtain p.value.internal, p.value.noadjust, and p.value.IvsE using Fisher's exact test. If FALSE, asymptotic tests will be used to calculate p-values.
weight.factor	internal use only.
Tbl	a 3 by 2 allele count table. The first column should have allele counts for the minor allele, and the second column should have allele counts for the major allele. The first, second and third row should correspond to case, internal control and external control, respectively.

Value

OR	OR estimate from iECAT.
SE	SE estimate of OR.
p.value	p-value of iECAT.
p.value.noadj	p-value without the adjustment of possible batch effects
p.value.internal	p-value with only internal study samples
p.value.IvsE	p-value of comparing internal vs external control samples

Author(s)

Seunggeun (Shawn) Lee

Examples

library(SKAT)

data(Example, package="iECAT")
attach(Example)

# iECAT-O
# test the second SNP in the first gene
idx.snp<-2

obj<-SKAT_Null_Model(Y ~ 1, out_type="D")
Z = Z.list[[1]][,idx.snp]
tbl.external= tbl.external.all.list[[1]][idx.snp,]


iECAT_SingleVar(Z, obj, tbl.external)

iECAT documentation built on May 2, 2019, 8:30 a.m.