GEWIST (version 1.16.0)

gewistLevene: Genome Environment Wide Interaction Search Threshold with Levene's test

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

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)