snp.tests.single-class {snpMatrix} | R Documentation

## Classes "snp.tests.single" and "snp.tests.single.score"

### Description

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 from the Class

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`

### Slots

`snp.names`:
  The names of the SNPs tested, as they appear as column names in the original `snp.matrix`
`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 `"snp.tests.single.score"`) Score statistics
`V`:
  (class `"snp.tests.single.score"`) Score variances

### Methods

[]
  `signature(x = "snp.tests.single", i = "ANY")`: Subsetting operator
[]
  `signature(x = "snp.tests.single.score", i = "ANY")`: Subsetting operator
chi.squared
  `signature(x = "snp.tests.single", df = "numeric")`: Extract 1- and 2-df chi-squared test values
effect.sign
  `signature(x = "snp.tests.single.score", simplify = "missing")`: Extract signs of associations tested by the 1df tests
names
  `signature(x="snp.tests.single")`: Extract names of test values (`snp.names` slot)
p.value
  `signature(x = "snp.tests.single", df = "numeric")`: Evaluate 1- and 2-df test p-values
show
  `signature(object = "snp.tests.single")`: List all tests and p-values
sample.size
  `signature(object = "snp.tests.single")`: Extract sample sizes for tests
effective.sample.size
  `signature(object = "snp.tests.single")`: 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 = "snp.tests.single")`: Summarize all tests and p-values
pool2
  `signature(x = "snp.tests.single.score", y = "snp.tests.single.score", score = "logical")`: Combine two sets of test results. Used recursively by {`pool`}
switch.alleles
  `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 tests

### Author(s)

David Clayton david.clayton@cimr.cam.ac.uk

### See Also

`single.snp.tests`, `pool`

### Examples

    showClass("snp.tests.single")
    showClass("snp.tests.single.score")

[Package snpMatrix version 1.8.0 Index]