iGasso (version 1.6.1)

VSTF.test: 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")

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.

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".

Author

Kai Wang <[e-mail]>

Details

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

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")