snp.tests.single-class {snpMatrix} | R Documentation |
These are classes to hold the objects created by
single.snp.tests
and provide methods for extracting key
elements. The class "snp.tests.single.score"
extends class
"snp.tests.single"
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("snp.tests.single", ...)
and
new("snp.tests.single.score", ...)
but, more usually, will be created
by calls to single.snp.tests
snp.names
:snp.matrix
chisq
:N
:N.r2
:N
and
the imputation r^2. Otherwise a zero-length objectU
:"snp.tests.single.score"
) Score statisticsV
:"snp.tests.single.score"
) Score variancessignature(x = "snp.tests.single", i = "ANY")
:
Subsetting operatorsignature(x = "snp.tests.single.score", i = "ANY")
:
Subsetting operatorsignature(x = "snp.tests.single", df =
"numeric")
:
Extract 1- and 2-df chi-squared test valuessignature(x = "snp.tests.single.score", simplify =
"missing")
: Extract signs of associations tested by the 1df testssignature(x="snp.tests.single")
: Extract names of
test values (snp.names
slot)signature(x = "snp.tests.single", df =
"numeric")
:
Evaluate 1- and 2-df test p-valuessignature(object = "snp.tests.single")
:
List all tests and p-valuessignature(object = "snp.tests.single")
:
Extract sample sizes for testssignature(object = "snp.tests.single")
:
Summarize all tests and p-valuessignature(x = "snp.tests.single.score",
y = "snp.tests.single.score", score = "logical")
: Combine two
sets of test results. Used recursively by {pool
}signature(x = "snp.tests.single.score", snps =
"ANY")
: Emulate, in the score vector and its (co)variances,
the effect of switching of the alleles for the specified testsDavid Clayton david.clayton@cimr.cam.ac.uk
showClass("snp.tests.single") showClass("snp.tests.single.score")