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- chi.squared
`signature(x = "SingleSnpTests", df = "numeric")`

: Extract 1- and 2-df chi-squared test values- effect.sign
`signature(x = "SingleSnpTestsScore", simplify = "missing")`

: Extract signs of associations tested by the 1df tests- names
`signature(x="SingleSnpTests")`

: Extract names of test values (`snp.names`

slot)- p.value
`signature(x = "SingleSnpTests", df = "numeric")`

: Evaluate 1- and 2-df test p-values- show
`signature(object = "SingleSnpTests")`

: List all tests and p-values- coerce
`signature(from = "SingleSnpTests", to = "data.frame")`

: Conversion to data frame class- sample.size
`signature(object = "SingleSnpTests")`

: Extract sample sizes for tests- effective.sample.size
`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- summary
`signature(object = "SingleSnpTests")`

: Summarize all tests and p-values- pool2
`signature(x = "SingleSnpTestsScore", y = "SingleSnpTestsScore", score = "logical")`

: Combine two sets of test results. Used recursively by`pool`

- switch.alleles
`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 [email protected]

1 2 |

snpStats documentation built on Nov. 1, 2018, 2:32 a.m.

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