SingleSnpTests-class: Classes "SingleSnpTests" and "SingleSnpTestsScore"
In snpStats: SnpMatrix and XSnpMatrix classes and methods

Description Objects from the Class Slots Methods Author(s) See Also Examples

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 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

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

[]: 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