sim.snp.expsurv.power {survSNP}

Asymptotic and Empirical Power

Description

This function calculates asymptotic and empirical power for SNP association studies

Usage

sim.snp.expsurv.power(GHR, B, n, raf, erate, pilm, lm, model, test, alpha, 
                      exactvar = FALSE, interval = c(0, 10), rootint = c(0.1, 200))

Arguments

GHR

Genotype Hazard Ratio

B

Number of simulation replicates (set to 0 if no empirical calculations are desired)

n

Sample size

raf

Relative risk allele frequency

erate

Event Rate

pilm

Probability that the time-to-event is greater than lm

lm

Landmark time used for powering the study

model

True genetic risk model (choices are "additive", "recessive" or "dominant". For the asymptotic calculations only the "additive" should be used until further notice)

test

Hypothesized genetic risk model (choices are "additive", "recessive" or "dominant". For the asymptotic calculations only the "additive" should be used until further notice)

alpha

Nominal two-sided type I error rate

exactvar

Indicator for using the exact variance formula

interval

Interval to search for baseline hazard rate

rootint

Interval to search for censoring bound

Details

This function calculates asymptotic and empirical power for SNP association studies

Value

This function returns a data.frame with the following columns

B

Number of simulation replicates

raf

Relative allelic frequency of the B allele

q0

Relative genotypic frequency for AA

q1

Relative genotypic frequency for AB

q2

Relative genotypic frequency for BB

lam0

Exponential hazard rate for P(T>t|AA)

lam1

Exponential hazard rate for P(T>t|AB)

lam2

Exponential hazard rate for P(T>t|BB)

GHR

Genotype Hazard Ratio

pilm

Probability that the time to event in the population exceeds the landmark lm: P(T>lm)

lm

Landmark (see pilm above)

model

The true genetic risk model

test

The hypothesized genetic risk model

a

Parameter for the censoring distribution (uniform on [a,b])

b

Parameter for the censoring distribution (uniform on [a,b])

erate

Event rate

n

Sample size

powB

Empirical Power

pow

Asymptotic Power based on the exact variance formula

pow0

Asymptotic Power based on the approximate variance formula

v1

First term of the variance (v1+v2+v12)

v2

Second term of the variance (v1+v2+v12)

v12

Third term (covariance) of the variance (v1+v2+v12)

Author(s)

Kouros Owzar, Zhiguo Li, Nancy Cox, Sin-Ho Jung and Chanhee Yi

References

Kouros Owzar, Zhiguo Li, Nancy Cox and Sin-Ho Jung. Power and Sample Size Calculations for SNP Association Studies with Censored Time-to-Event Outcomes. https://onlinelibrary.wiley.com/doi/full/10.1002/gepi.21645

See Also

survSNP.power.table

Examples

# See vignette for examples including details on the example
# considered below

results<-sim.snp.expsurv.power(GHR=1.25, B=0, n=500, raf=0.1, erate=0.75, pilm=0.5, 
                               lm=1, model="additive", test="additive", alpha=0.05)
results[,c("n","erate","alpha","pow0")]