IndOR: SNPxSNP interaction testing based on odds-ratio

In MathieuEmily/IndOR: Testing for SNPxSNP Interaction with the IndOR method

Description

IndOR allows the search for SNP-SNP epistasis, i.e., for an association between a case-control phenotype and the interaction between two biallelic SNPs.

Usage

IndOR(x)

Arguments

x	A 9x2 matrix or data.frame

Details

IndOR is an implementation of the test proposed in Emily (2012). The procedure is based on the testing of the independence between odds-ratio. A matrix of genotype counts, x is taken as input. Dimensions for x should be 9 rows and 2 columns. Each column corresponds to the disease status (for example the first column for cases and the second column for controls). Each row corresponds to pair of genotypes as follows. If a (resp. b) is the minor allele for the first (resp. second) SNP then rows for x should be ordered as (AABB,AABb,AAbb,AaBB,AaBb,Aabb,aaBB,aaBb,aabb).

Value

A list containing the following components:

statistic	The value of the test statistic
p.value	The p-value for the test

References

Mathieu Emily (2012) IndOR: A new statistical procedure to test for SNP-SNP epistasis in Genome-Wide Association Studies, Statistics In Medicine, 31(21) :2359-2373

Examples

## Example of genotype counts in cases and controls
Cases <- c(349,299,64,466,399,86,155,133,49)
Controls <- c(353,302,65,470,403,56,157,134,29)

## Counts are summarized in 9x2 matrix
x <- cbind(Cases,Controls)

## Test computation
IndOR(x)

MathieuEmily/IndOR documentation built on May 7, 2019, 4:33 p.m.