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)

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

showClass("GlmTests")