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snpStats (version 1.22.0)

GlmTests-class: Classes "GlmTests" and "GlmTestsScore"

Description

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)

Arguments

Objects from the Class

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

Methods

[]
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

See Also

snp.lhs.tests,snp.rhs.tests, SingleSnpTests, SingleSnpTestsScore

Examples

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showClass("GlmTests")

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