MiRKAT.Q: Robust MiRKAT (quantile regression)

In MiRKAT: Microbiome Regression-Based Kernel Association Tests

Robust MiRKAT (quantile regression)

Description

A more robust version of MiRKAT utlizing a linear model that uses quantile regression.

Usage

MiRKAT.Q(y, X, Ks, omnibus = "kernel_om", returnKRV = FALSE, returnR2 = FALSE)

Arguments

y	A numeric vector of the a continuous or dichotomous outcome variable.
X	A numerical matrix or data frame, containing additional covariates that you want to adjust for. Mustn't be NULL.
Ks	A list of n by n kernel matrices (or a single n by n kernel matrix), where n is the sample size. If you have distance metric from metagenomic data, each kernel can be constructed through function D2K. Each kernel can also be constructed through other mathematical approaches, such as linear or Gaussian kernels.
omnibus	A string equal to either "Cauchy" or "kernel_om" (or nonambiguous abbreviations thereof), specifying whether to use the Cauchy combination test or an omnibus kernel to generate the omnibus p-value.
returnKRV	A logical indicating whether to return the KRV statistic. Defaults to FALSE.
returnR2	A logical indicating whether to return the R-squared coefficient. Defaults to FALSE.

Details

MiRKAT.Q creates a kernel matrix using the linear model created with the function rq, a quantile regression function, then does the KRV analysis on Ks and the newly formed kernel matrix representing the outome traits.

Missing data is not permitted. Please remove all individuals with missing y, X, Ks prior to analysis

Value

Returns p-values for each individual kernel matrix, an omnibus p-value if multiple kernels were provided, and measures of effect size KRV and R2.

p_values	labeled individual p-values for each kernel
omnibus_p	omnibus p_value, calculated as for the KRV test
KRV	A vector of kernel RV statistics (a measure of effect size), one for each candidate kernel matrix. Only returned if returnKRV = TRUE
R2	A vector of R-squared statistics, one for each candidate kernel matrix. Only returned if returnR2 = TRUE

Author(s)

Weija Fu

Examples

    
library(GUniFrac)
library(quantreg)

# Generate data
data(throat.tree)
data(throat.otu.tab)
data(throat.meta)

unifracs = GUniFrac(throat.otu.tab, throat.tree, alpha = c(1))$unifracs
if (requireNamespace("vegan")) {
 library(vegan)
 BC= as.matrix(vegdist(throat.otu.tab, method="bray"))
 Ds = list(w = unifracs[,,"d_1"], uw = unifracs[,,"d_UW"], BC = BC)
} else {
 Ds = list(w = unifracs[,,"d_1"], uw = unifracs[,,"d_UW"])
}
Ks = lapply(Ds, FUN = function(d) D2K(d))

covar = scale(cbind(throat.meta$Age, as.numeric(throat.meta$Sex == "Male")))

# Continuous phenotype
n = nrow(throat.meta)
y = rchisq(n, 2) + apply(covar, 1, sum) 
MiRKAT.Q(y, X = covar, Ks = Ks)

MiRKAT documentation built on March 7, 2023, 5:55 p.m.