GlmTests-class: Classes "GlmTests" and "GlmTestsScore"
In snpStats: SnpMatrix and XSnpMatrix classes and methods

Description Objects from the Class Methods Note Author(s) See Also Examples

Classes of objects created by snp.lhs.tests and snp.rhs.tests. The class "GlmTestsScore" extends the class "GlmTests" and is invoked by setting the argument score=TRUE when calling testing functions in order to save the scores and their variances (and covariances)

Objects of class "GlmTests" have four slots:

snp.names: When only single SNPs are tested, a character vector of SNP names. Otherwise a list of such vectors (one for each test)
var.names: A character vector containing names of variables tested against SNPs
chisq: A numerical vector of chi-squared test values
df: An integer vector of degrees of freedom for the tests
N: A integer vector of the number of samples contributing to each test

The "GlmTestsScore" class extends this, adding a slot score containing a list with elements which are themselves lists with two elements:

U: The vector (or matrix) of efficient scores
V: The upper triangle of the variance-covariance matrix of U, stored as a vector

[]: signature(x = "GlmTests", i = "ANY", j = "missing", drop = "missing"): Subsetting operator
coerce: signature(from = "GlmTests", to = "data.frame"): Simplify object
chi.squared: signature(x = "GlmTests", df = "missing"): Extract chi-squared test values
deg.freedom: signature(x = "GlmTests"): Extract degrees of freedom for tests
names: signature(x="GlmTests"): Extract (or generate) a name for each test
p.value: signature(x = "GlmTests", df = "missing"): Extract p-values
sample.size: signature(object = "GlmTests"): Extract sample sizes for tests
show: signature(object = "GlmTests"): Show method
summary: signature(object = "GlmTests"): Summary method
[]: signature(x = "GlmTestsScore", i = "ANY", j = "missing", drop = "missing"): Subsetting operator
effect.sign: signature(x = "GlmTestsScore", simplify = "logical"): Extract signs of associations. If simpify is TRUE then a simple vector is returned if all tests are on 1df
pool2: signature(x = "GlmTestsScore", y = "GlmTestsScore", score = "logical"): Combine results from two sets of tests
switch.alleles: signature(x = "GlmTestsScore", snps = "character"): Emulate, in the score vector and its (co)variances, the effect of switching of the alleles of specified SNPs