gewistLevene: Genome Environment Wide Interaction Search Threshold with...

In GEWIST: Gene Environment Wide Interaction Search Threshold

Description

Compute the optimal Variance Prioritization power and the corresponding Levene's test prioritization p-value threshold for a given interaction effect size

Usage

gewistLevene(p, N, theta_gc, theta_c, M, K = 20000, verbose = FALSE)

Arguments

p	minor allele frequency of the SNP, a number between 0 and 0.5
N	sample size
theta_gc	proportion of quantitative trait variance explained by the interaction, should be a number between 0 and 1
theta_c	proportion of quantitative trait variance explained by the covariate, should be a number between 0 and 1
M	total number of SNPs to be tested
K	number of procedures, by default, set to be 20,000
verbose	logical; if TRUE, function returns a data.frame class object listing the VP power at each p-value, from 0.001 to 1 with 0.001 incremental increase.

Value

A list with three components:

Optimal_VP_power	VP power to detect interactions at the optimal Levene's test p-value threshold
Conventional_power	power to detect interactions without prioritization, i.e, VP power at Levene's test p-value of 1
Optimal_pval_threshold	levene'e test p-value at which optimal VP power is achieved

Author(s)

Wei Q. Deng <[e-mail]> Guillaume Pare <[e-mail]>

References

Deng W.Q, Pare G. (2011) A fast algorithm to optimize SNP prioritization for gene-gene and gene-environment interactions. Genetic Epidemiology 35: 729-738. doi: 10.1002/gepi.20624

Pare G, Cook NR, Ridker PM, Chasman DI (2010) On the Use of Variance per Genotype as a Tool to Identify Quantitative Trait Interaction Effects: A Report from the Women's Genome Health Study. PLoS Genet 6(6): e1000981. doi:10.1371/journal.pgen.1000981

Levene H. (1960) Robust tests for equality of variances. In Contributions to Probability and Statistics: Essays in Honor of Harold Hotelling eds:I. Olkin, S.G. Ghurye, W. Hoeffding, W.G. Madow & H.B.Mann, pp.278-292. Stanford: Stanford University Press.

Examples

# Given a SNP with minor allele frequency of 10% and a sample 
# of 15,000 individuals, we are interested in testing interactions
# between this SNP and a covariate of effect size #10%. The 
# total number of SNP is 500,000. Assume the interaction 
# explains 0.1% of the quantitative trait variance. 


library(GEWIST)
gewistLevene(p = 0.1, N = 15000, theta_gc =0.1/100, theta_c = 0.1 , M = 500000, 
K = 20000, verbose=FALSE)

GEWIST documentation built on Nov. 8, 2020, 5:46 p.m.