`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)
`"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

`"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

`snp.lhs.tests`

,`snp.rhs.tests`

,
`SingleSnpTests`

,
`SingleSnpTestsScore`