trio.power {trio} | R Documentation

## Power and sample size calculation

### Description

Computes power for genotypic TDT, allelic TDT or Score test given n trios or required sample size to gain given power.

### Usage

    trio.power(maf = 0.5, RR = 1.5, alpha = 5*10^(-8), n = NULL, beta = NULL,
      model = c("additive", "dominant", "recessive"), test = c("gTDT", "Score", "aTDT"))

    ## S3 method for class 'trio.power'
    print(x,digits=4,...)

### Arguments

`maf` | a numeric vector of population frequencies of a mutant allele.
`RR` | a numeric vector of the assumed relative risks for an individual getting a disease with 1 (in case of recessive model 2) mutant alleles compared to the risk of individuals carnying 0 mutant alleles.
`alpha` | a numeric vector of significance levels (Type I Error probability).
`n` | a numeric vector containing number of trios in a study. Must be filled for power calculation. Must not be NULL for sample size calculation.
`beta` | the desired power of the test. Must be filled for power calculation. Must not be NULL for sample size calculation.
`model` | a character containing the genotypic model assumed. Possible values are `"additive"`, `"dominant"` and `"recessive"`. In case of `test="aTDT"`, the standard multiplicative model will be considered. Abbreviations are allowed. Thus, e.g., `model = "dom"` will fit a dominant model, and `model = "r"` a recessive model.
`test` | the chosen test. Must be `"aTDT"`, `"gTDT"` or `"Score"`. Abbreviations are allowed. Thus, e.g., `test = "g"` will perform a genotypic TDT, and `test = "S"` a Score test.
`x` | an object of class `trio.power`.
`digits` | number of digits that should be printed.
`...` | ignored

### Details

Power and sample size calculation is derived on Knapp (1999). The power or the sample size will be calculated for all combinations of p, RR, alpha, test, model and n or beta.

### Value

An object of class trio.power containing the following numeric values or vectors, respectively:

`model` | the chosen model
`size` | In case of sample size calculation: calculated sample sizes
`beta` | In case of sample size calculation: desired power
`n` | In case of power calculation: given number of trios
`power` | In case of power calculation: calculated power
`alpha` | Type I error
`test` | the chosen test
`RR` | the relative risks assumed
`p` | the assumed allele frequency
`calc` | the type of calculation

### Author(s)

Christoph Neumann

### References

Knapp, M. (1999). A Note on Power Approximations for the Transmission/Disequilibrium Test. American Journal of Human Genetics, 64, 1177-1185.

Neumann, C., Taub, M.A., Younkin, S.G., Beaty, T.H., Ruczinski, I., Schwender, H. (2014). Analytic Power and Sample Size Calculation for the Genotypic Transmission/Disequilibrium Test in Case-Parent Trio Studies. Submitted.

### Examples

    # The required samples size to reach of power
    # of 0.8 when testing SNPs with minor allele
    # frequencies of 0.1 and 0.2 with an additive
    # or dominant genotypic TDT and score test
    # can be determined by
    trio.power(maf = c(0.1, 0.2), beta = 0.8, model = c("add", "dom"))

[Package trio version 3.22.0 Index]