SPAr (version 0.1)

SPA.I.GE: Rare variants association test score to evaulate the effect of gene-environmental interactions

Description

Compute the nonparametric association information score between a set of rare variants and dichotomous outcomes, incorporating interactions with environmental factors.

Usage

SPA.I.GE(x, y, E, nperm = 100)

Arguments

x

a matrix of numeric genotypes with each row as an individual and each column as a separate rare SNP. Each genotype should be coded as 0,1 and 2.

y

a vector of phenotypes. The length of y should be the same as the number of rows of x.

E

a vector of environmental factors. It must be a categorical variable.

nperm

the number of permutations used to obtain the significance level. See details.

Value

I2star

The numerical value of the information score.

pvalue.global

The p-value from global permutation.

pvalue.local

The p-value from local permutation.

call

The matched call.

type

Type of the method used. It is "env".

Details

This function evaluates the gene-environmental intearction effects associated with the dichotomous trait. The phenotype y must be dichotomous. The significance is computed using both global permutation and local permutation.

References

Fan, R., Lo, S-H (2013). A robust model-free approach for rare variantss association studies incorporating gene-gene and gene-environmental interactions. PLOS ONE 8(12):e83057.

Examples

	data(SPA_example)
	attach(SPA_example)
	SPA.I.GE <- SPA.I.GE(x,y.d,E,nperm=10)
	print(SPA.I.GE)