npt {AssocTests}

Nonparametric trend test based on the nonparametric risk under a given genetic model

Description

Test for the association between a genetic variant and a non-normal distributed quantitative trait based on the nonparametric risk under a specific genetic model.

Usage

npt(y, g, varphi)

Arguments

y

a numeric vector of the observed quantitative trait values in which the ith element corresponds to the trait value of the ith subject.

g

a numeric vector of the observed genotype values (0, 1, or 2 denotes the number of risk alleles) in which the ith element is the genotype value of the ith subject for a biallelic SNP. g has the same length as y.

varphi

a numeric value which represents the genetic model. It should be 0, 0.5, or 1, which indicates that the calculation is performed under the recessive, additive, or dominant model, respectively.

Details

For a non-normal distributed quantitative trait, three genetic models (recessive, additive and dominant) used commonly are defined in terms of the nonparametric risk (NR). The recessive, additive, and dominant models can be classified based on the nonparametric risks. More specifically, the recessive, additive, and dominant models refer to NR20 > NR10 = 1/2, NR12 = NR10>1/2, and NR10 = NR20 > 1/2, respectively, where NR10 and NR20 are the nonparametric risks of the groups with the genotypes 1 and 2 relative to the group with the genotype 0, respectively, and NR12 is the nonparametric risk of the group with the genotype 2 relative to the group with the genotype 1.

varphi can be 0, 0.5, or 1 for the recessive, additive, or dominant model, respectively. When varphi is 0, the test is constructed under the recessive model by pooling together the subjects with the genotypes 0 and 1. Similarly, when varphi is 1, the test is constructed under the dominant model by pooling together the subjects with the genotypes 1 and 2. When varphi is 0.5, the test is based on the weighted sum of NR10 and NR12.

Value

A list with class "htest" containing the following components:

statistic
			the observed value of the test statistic.
p.value
			the p-value for the test.
alternative
			a character string describing the alternative hypothesis.
method
			a character string indicating the type of test performed.
data.name
			a character string giving the names of the data.

Author(s)

Lin Wang, Wei Zhang, and Qizhai Li.

References

Lin Wang, Wei Zhang, and Qizhai Li. AssocTests: An R Package for Genetic Association Studies. Journal of Statistical Software. 2020; 94(5): 1-26.

Examples

g <- rbinom(1500, 2, 0.3)
y <- 0.5 + 0.25 * g + rgev(1500, 0, 0, 5)
npt(y, g, 0.5)