Classes of objects created by snp.lhs.tests
and snp.rhs.tests. The class
"GlmTestsScore" extends the class
"GlmTests" and is invoked by setting the argument
score=TRUE when calling testing functions
in order to save the scores and their variances
(and covariances)
Objects from the Class
Objects of class "GlmTests"
have four slots:
snp.names
When only single SNPs are tested,
a character vector of SNP names. Otherwise a list
of such vectors (one for each test)
var.names
A character vector containing names of variables
tested against SNPs
chisq
A numerical vector of chi-squared test values
df
An integer vector of degrees of freedom for the tests
N
A integer vector of the number of samples contributing to
each test
The "GlmTestsScore" class extends this, adding a slot
score containing a list with elements which are themselves
lists with two elements:
U
The vector (or matrix) of efficient scores
V
The upper triangle of the variance-covariance matrix of
U, stored as a vector
Methods
[]
signature(x = "GlmTests", i = "ANY", j =
"missing", drop = "missing"): Subsetting operator
coerce
signature(from = "GlmTests", to = "data.frame"):
Simplify object
chi.squared
signature(x = "GlmTests", df =
"missing"): Extract chi-squared test values
deg.freedom
signature(x = "GlmTests"): Extract
degrees of freedom for tests
names
signature(x="GlmTests"): Extract (or generate)
a name for each test
signature(object = "GlmTests"):
Extract sample sizes for tests
show
signature(object = "GlmTests"): Show method
summary
signature(object = "GlmTests"): Summary
method
[]
signature(x = "GlmTestsScore", i = "ANY", j =
"missing", drop = "missing"): Subsetting operator
effect.sign
signature(x = "GlmTestsScore", simplify =
"logical"): Extract signs of associations. If simpify is
TRUE then a simple vector is returned if all tests are on 1df
pool2
signature(x = "GlmTestsScore", y =
"GlmTestsScore", score = "logical"): Combine results from two
sets of tests
switch.alleles
signature(x = "GlmTestsScore", snps =
"character"): Emulate, in the score vector and its (co)variances,
the effect of switching of the alleles of specified SNPs
Note
Most of the methods for this class are shared with
the SingleSnpTests and
SingleSnpTestsScore classes
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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> library(snpStats)
Loading required package: survival
Loading required package: Matrix
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/snpStats/GlmTests-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GlmTests-class
> ### Title: Classes "GlmTests" and "GlmTestsScore"
> ### Aliases: GlmTests-class [,GlmTests,ANY,missing,missing-method
> ### chi.squared,GlmTests,missing-method deg.freedom,GlmTests-method
> ### effect.sign,GlmTests,logical-method names,GlmTests-method
> ### coerce,GlmTests,data.frame-method p.value,GlmTests,missing-method
> ### sample.size,GlmTests-method show,GlmTests-method
> ### summary,GlmTests-method GlmTestsScore-class
> ### [,GlmTestsScore,ANY,missing,missing-method
> ### pool2,GlmTestsScore,GlmTestsScore,logical-method
> ### switch.alleles,GlmTestsScore,character-method
> ### Keywords: classes
>
> ### ** Examples
>
> showClass("GlmTests")
Class "GlmTests" [package "snpStats"]
Slots:
Name: snp.names var.names chisq df N
Class: ANY character numeric integer integer
Known Subclasses: "GlmTestsScore"
>
>
>
>
>
> dev.off()
null device
1
>