pleio.q.test {pleio}

Single test of the number of traits associated with genotype

Description

Perform single test of the number of traits associated with a genotype, by allowing a specified number of regression beta's to be unconstrained.

Usage

pleio.q.test(obj.fit, count.nonzero.beta = 0)

Arguments

obj.fit

result of pleio.q.fit

count.nonzero.beta

Number of non-zero betas. A non-zero beta is allowed to be unconstrained, while all other beta's are constrained to be zero.

Details

By specifying the number of non-zero beta's, the algorithm evaluates all possible ways of choosing unconstrained and constrained beta's, and for each configuration a statistic (tk) is computed. This tk statistic can be considered a measure of fit of a model. The minimum tk over all possible configurations provides a global test of whether one of the models fits well.

Value

A list containing:

stat

global test statistict

df

degrees of freedom of the statistic

pval

p-value for the test

index.nonzero.beta

index of the non-zero beta(s) that provide(s) the minimum tk goodness of fit statistic - this configuration is assumed to have beta's for all other indices equal to zero.

tests

data.frame containing the tests performed. For m traits, and k = count.nonzero.beta, there are m-choose-k tests considered in the null hypothesis. The data.frame provides the indices of the unconstrained betas and the corresponding tk test statistic for the configuration.

Author(s)

Dan Schaid and Jason Sinnwell

References

Schaid DJ, Tong X, Larrabee B, Kennedy RB, Poland GA, Sinnwell JP. Statistical Methods for Testing Genetic Pleiotropy. Genetics. 2016 Oct;204(2):483-497.

Examples

data(pleio.qdemo)
fit <- pleio.q.fit(y, geno)
## usual multivariate test of whether all betas = 0
test0 <- pleio.q.test(fit, count.nonzero.beta = 0)
test0
## test whether allowing 2 betas to be non-zero fits data
test2 <- pleio.q.test(fit, count.nonzero.beta = 2)
test2