VSTF.test: Association Tests for Rare Variants Based on...
In iGasso: Statistical Tests and Utilities for Genetic Association

View source: R/VSTF.test.R

VSTF.test

R Documentation

Association Tests for Rare Variants Based on Variance-Stabilizing Transformation

Description

VSTF.test performs tests on association between a rare variant and case-control status using a variance-stabilizing transformation.

Usage

VSTF.test(G, method = "Anscombe")

Arguments

`G`	a `2x2` matrix. The first row is for cases and the second one for controls. In each row, the first element is the number of non-carriers and the second one is the number of carriers with at least 1 copy of the variant.
`method`	a character string indicating which transformation to use. One of `"Anscombe"` (default), `"arcsine"`, `"Freeman-Tukey"`, and `"Chanter"`.

Details

Each test is named after the author(s) of the corresponding publication.

Value

A list with class "test" containing the following components: * statistic the value of the test statistic. * p.value the p-value for the test computed from a chi-square distribution with 1 df. * method a character string indicting the test performed. * data.name a character string giving the name of the data.

Author(s)

Kai Wang <kai-wang@uiowa.edu>

References

Anscombe, F. J. (1948) The transformation of Poisson, binomial and negative-binomial data. Biometrika 35(3/4), 246–254.

Chanter, D. O. (1975). Modifications of the angular transformation. Journal of the Royal Statistical Society. Series B (Applied Statistics) 24(3), 354–359.

Freeman, M. F., Tukey, J. W. (1950) Transformations related to the angular and the square root. The Annals of Mathematical Statistics 21(4), 607–611.

Wang, K., Fingert, J. (2012) Statistical tests for detecting rare variants using variance-stabilizing transformations. Annals of Human Genetics. 76(5):402-409.

Zar, J.H. (1999) Biostatistical Analysis, 4th ed., New Jersey:Prentice-Hall, Inc.

Examples

## Example 1 of Li et al. (2010)
G = rbind(c(14, 999), c(3, 1081))
VSTF.test(G)
VSTF.test(G, method = "arcsine")
VSTF.test(G, method = "Freeman-Tukey")

iGasso documentation built on Aug. 8, 2023, 5:11 p.m.