trio.power {trio} | R Documentation |
Computes power for genotypic TDT, allelic TDT or Score test given n trios or required sample size to gain given power.
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,...)
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 |
test |
the chosen test. Must be |
x |
an object of class |
digits |
number of digits that should be printed. |
... |
ignored |
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.
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 |
Christoph Neumann
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.
# 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"))