snp.lhs.tests {snpMatrix}R Documentation

Score tests with SNP genotypes as dependent variable

Description

Under the assumption of Hardy-Weinberg equilibrium, a SNP genotype is a binomial variate with two trials for an autosomal SNP or with one or two trials (depending on sex) for a SNP on the X chromosome. With each SNP in an input "snp.matrix" as dependent variable, this function first fits a "base" logistic regression model and then carries out a score test for the addition of further term(s). The Hardy-Weinberg assumption can be relaxed by use of a "robust" option.

Usage

snp.lhs.tests(snp.data, base.formula, add.formula, subset, snp.subset,
                data = sys.parent(), robust = FALSE,
                control=glm.test.control(maxit=20, epsilon=1.e-4,R2Max=0.98),
                score=FALSE)

Arguments

snp.data The SNP data, as an object of class "snp.matrix" or "X.snp.matrix"
base.formula A formula object describing the base model, with dependent variable omitted
add.formula A formula object describing the additional terms to be tested, also with dependent variable omitted
subset An array describing the subset of observations to be considered
snp.subset An array describing the subset of SNPs to be considered. Default action is to test all SNPs.
data The data frame in which base.formula, add.formula and subset are to be evaluated
robust If TRUE, a test which does not assume Hardy-Weinberg equilibrium will be used
control An object giving parameters for the IRLS algorithm fitting of the base model and for the acceptable aliasing amongst new terms to be tested. See code{glm.test.control}
score Is extended score information to be returned?

Details

The tests used are asymptotic chi-squared tests based on the vector of first and second derivatives of the log-likelihood with respect to the parameters of the additional model. The "robust" form is a generalized score test in the sense discussed by Boos(1992). If a data argument is supplied, the snp.data and data objects are aligned by rowname. Otherwise all variables in the model formulae are assumed to be stored in the same order as the columns of the snp.data object.

Value

An object of class snp.tests.glm or snp.tests.glm.score depending on whether score is set to FALSE or TRUE in the call.

Note

A factor (or several factors) may be included as arguments to the function strata(...) in the base.formula. This fits all interactions of the factors so included, but leads to faster computation than fitting these in the normal way. Additionally, a cluster(...) call may be included in the base model formula. This identifies clusters of potentially correlated observations (e.g. for members of the same family); in this case, an appropriate robust estimate of the variance of the score test is used.

Author(s)

David Clayton david.clayton@cimr.cam.ac.uk

References

Boos, Dennis D. (1992) On generalized score tests. The American Statistician, 46:327-333.

See Also

snp.tests.glm-class, snp.tests.glm.score-class, glm.test.control,snp.rhs.tests single.snp.tests, snp.matrix-class, X.snp.matrix-class

Examples

data(testdata)
snp.lhs.tests(Autosomes[,1:10], ~cc, ~region, data=subject.data)
snp.lhs.tests(Autosomes[,1:10], ~strata(region), ~cc,
   data=subject.data)

[Package snpMatrix version 1.6.1 Index]