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 1.6.1 Index]