snpStats (version 1.22.0)

SingleSnpTests-class: Classes "SingleSnpTests" and "SingleSnpTestsScore"

Description

These are classes to hold the objects created by single.snp.tests and provide methods for extracting key elements. The class "SingleSnpTestsScore" extends class "SingleSnpTests" to include the score and score variance statistics in order to provide methods for pooling results from several studies or parts of a study

Objects from the Class

Objects can be created by calls of the form new("SingleSnpTests", ...) and new("SingleSnpTestsScore", ...) but, more usually, will be created by calls to single.snp.tests

Slots

snp.names:

The names of the SNPs tested, as they appear as column names in the original SnpMatrix

chisq:

A two-column matrix holding the 1 and 2 df association tests

N:

The numbers of observations included in each test

N.r2:

For tests on imputed SNPs, the product of N and the imputation $r^2$. Otherwise a zero-length object

U:

(class "SingleSnpTestsScore") Score statistics

V:

(class "SingleSnpTestsScore") Score variances

Methods

[]

signature(x = "SingleSnpTests", i = "ANY"): Subsetting operator

[]

signature(x = "SingleSnpTestsScore", i = "ANY"): Subsetting operator

chi.squared

signature(x = "SingleSnpTests", df = "numeric"): Extract 1- and 2-df chi-squared test values

effect.sign

signature(x = "SingleSnpTestsScore", simplify = "missing"): Extract signs of associations tested by the 1df tests

names

signature(x="SingleSnpTests"): Extract names of test values (snp.names slot)

p.value

signature(x = "SingleSnpTests", df = "numeric"): Evaluate 1- and 2-df test p-values

show

signature(object = "SingleSnpTests"): List all tests and p-values

coerce

signature(from = "SingleSnpTests", to = "data.frame"): Conversion to data frame class

sample.size

signature(object = "SingleSnpTests"): Extract sample sizes for tests

effective.sample.size

signature(object = "SingleSnpTests"): Extract effective sample sizes for tests. For imputed tests, these are the real sample sizes multiplied by the corresponding R-squared values for imputation

summary

signature(object = "SingleSnpTests"): Summarize all tests and p-values

pool2

signature(x = "SingleSnpTestsScore", y = "SingleSnpTestsScore", score = "logical"): Combine two sets of test results. Used recursively by pool

switch.alleles

signature(x = "SingleSnpTestsScore", snps = "ANY"): Emulate, in the score vector and its (co)variances, the effect of switching of the alleles for the specified tests

See Also

single.snp.tests, pool

Examples

showClass("SingleSnpTests")
showClass("SingleSnpTestsScore")