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
signature(x = "SingleSnpTests", df =
"numeric")
:
Extract 1- and 2-df chi-squared test values
signature(x = "SingleSnpTestsScore", simplify =
"missing")
: Extract signs of associations tested by the 1df tests
signature(x="SingleSnpTests")
: Extract names of
test values (snp.names
slot)
signature(x = "SingleSnpTests", df =
"numeric")
:
Evaluate 1- and 2-df test p-values
signature(object = "SingleSnpTests")
:
List all tests and p-values
signature(from = "SingleSnpTests", to = "data.frame")
:
Conversion to data frame class
signature(object = "SingleSnpTests")
:
Extract sample sizes for tests
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
signature(object = "SingleSnpTests")
:
Summarize all tests and p-values
signature(x = "SingleSnpTestsScore",
y = "SingleSnpTestsScore", score = "logical")
: Combine two
sets of test results. Used recursively by pool
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
David Clayton dc208@cam.ac.uk
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