GlmTests-class {snpStats} | R Documentation

## 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

### Note

Most of the methods for this class are shared with the `SingleSnpTests` and `SingleSnpTestsScore` classes

### Author(s)

David Clayton dc208@cam.ac.uk

### See Also

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

### Examples

    showClass("GlmTests")

[Package snpStats version 1.40.0 Index]