snp.tests.glm-class {snpMatrix} | R Documentation

## Classes "snp.tests.glm" and "snp.tests.glm.score"

### Description

Classes of objects created by `snp.lhs.tests` and `snp.rhs.tests`. The class `"snp.tests.glm.score"` extends the class `"snp.tests.glm"` 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 `"snp.tests.glm"` have four slots:

test.names
  A character vector of names
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 `"snp.tests.glm.score"` class extends this, adding a slot `score` containing a list with elements which are themselves lists with two elements:

U
  The vector of efficient scores
V
  The upper triangle of the variance-covariance matrix of `U`, stored as a vector

### Methods

[
  `signature(x = "snp.tests.glm", i = "ANY", j = "missing", drop = "missing")`: Subsetting operator
chi.squared
  `signature(x = "snp.tests.glm", df = "missing")`: Extract chi-squared test values
deg.freedom
  `signature(x = "snp.tests.glm")`: Extract degrees of freedom for tests
names
  `signature(x="snp.tests.glm")`: Extract names of test values (`test.names` slot)
p.value
  `signature(x = "snp.tests.glm", df = "missing")`: Extract p-values
sample.size
  `signature(object = "snp.tests.glm")`: Extract sample sizes for tests
show
  `signature(object = "snp.tests.glm")`: Show method
summary
  `signature(object = "snp.tests.glm")`: Summary method
[
  `signature(x = "snp.tests.glm.score", i = "ANY", j = "missing", drop = "missing")`: Subsetting operator
effect.sign
  `signature(x = "snp.tests.glm.score", 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 = "snp.tests.glm.score", y = "snp.tests.glm.score", score = "missing")`: Combine results from two sets of tests
switch.alleles
  `signature(x = "snp.tests.glm.score", 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 `snp.tests.single` and `snp.tests.single.score` classes

### Author(s)

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

### See Also

`snp.lhs.tests`,`snp.rhs.tests`, `snp.tests.single`, `snp.tests.single.score`

### Examples

    showClass("snp.tests.glm")

[Package snpMatrix version 1.8.0 Index]