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

Arguments

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

Run this code
showClass("SingleSnpTests")
showClass("SingleSnpTestsScore")

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