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 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

- []
`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- p.value
`signature(x = "GlmTests", df = "missing")`

: Extract*p*-values- sample.size
`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

Most of the methods for this class are shared with
the `SingleSnpTests`

and
`SingleSnpTestsScore`

classes

David Clayton dc208@cam.ac.uk

`snp.lhs.tests`

,`snp.rhs.tests`

,
`SingleSnpTests`

,
`SingleSnpTestsScore`

1 | ```
showClass("GlmTests")
``` |

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