ZINQ_combination: Combine the marginal p-values

In wdl2459/ZINQ-v2: Zero-Inflated Quantile Approach for Microbiome Association Testing

Combine the marginal p-values

Description

Combine the marginal p-values

Usage

ZINQ_combination(
  input,
  method = "MinP",
  taus = c(0.1, 0.25, 0.5, 0.75, 0.9),
  M = 10000
)

Arguments

input	An output from ZINQ_tests.
method	Combination method, "MinP" for MinP test, "Cauchy" for Cauchy combination test; default is "MinP".
taus	A grid of quantile levels, must be a subset or equal to that from input; default is c(0.1, 0.25, 0.5, 0.75, 0.9).
M	The number of MC draws from the joint distribution of quantile rank-scores when method is "MinP"; default is 10000.

Details

• Please choose 'MinP' or 'Cauchy' for method, no other options.

• taus must be a subset or equal to the grid used to produce input.

Value

A pvalue, the final p-value of ZINQ.

References

• Ling, W. et al. (2021). Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ). Microbiome 9, 181.

• He, Z. et al. (2017). Unified sequence-based association tests allowing for multiple functional annotations and meta-analysis of noncoding variation in metabochip data. The American Journal of HumanGenetics 101(3), 340–352.

• Lee, S. et al. (2012). Optimal tests for rare variant effects in sequencing association studies. Biostatistics 13(4), 762–775.

• Liu, Y., Xie, J. (2019). Cauchy combination test: a powerful test with analytic p-value calculation under arbitrary dependency structures. Journal of the American Statistical Association, 1–18.

Examples

n = 300
p <- function(x0, gam0=0.75, gam1=-0.15){
  lc = gam0 + gam1*x0
  exp(lc) / (1 + exp(lc))
}
x = c(rep(0, n), rep(1, n))
w = 0.5 + 1.5*x + (1+0.15*x)*rchisq(2*n,df=1)
b = rbinom(2*n, 1, p(x))
y = w*b
dat = data.frame(y, x)

result = ZINQ_tests(formula.logistic=y~x, formula.quantile=y~x, C="x", data=dat)
ZINQ_combination(result, method="Cauchy")

wdl2459/ZINQ-v2 documentation built on March 25, 2024, 6:23 p.m.