survSNP.power.table: Table for Asymptotic and Empirical Power

In survSNP: Power Calculations for SNP Studies with Censored Outcomes

Table for Asymptotic and Empirical Power

Description

This function produces a table with the resulting empirical and asymptotic power over a given range of Genotype Hazard Ratios, relative allelic frequencies, sample sizes, and event rates.

Usage

survSNP.power.table(GHRs, ns, rafs, erates, pilm, lm, model, test, alpha, 
                    exactvar = FALSE, B = 0)

Arguments

GHRs	A vector of Genotype Hazard Ratios
ns	A vector of sample sizes
rafs	A vector of relative allelic frequencies (for the risk allele)
erates	A vector of event rates
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
B	Number of simulation replicates (set to 0 if no empirical calculations are desired)

Details

This version only supports additive models.

Value

See output of sim.snp.expsurv.power.

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

Examples

GRRs<-seq(1.5,2,by=0.25)
ns<-c(100,500,1000)
rafs<-c(0.3,0.5,0.7)
erates=c(0.5,0.7,0.9)
res<-survSNP.power.table(GRRs,ns,rafs,erates,pilm=0.5,lm=1,model="additive",
                         test="additive",alpha=0.05)

# Create key for illustration
KEY=paste("q=",levels(factor(res$raf)),sep="")
KEY<-list(lines=list(col=1:length(KEY),lty=1:length(KEY)),
          text=list(labels=paste("q=",levels(factor(res$raf)),sep="")),
          column=3)


# Illustrate Power
print(xyplot(pow0~GHR|factor(erate)*factor(n),group=factor(raf),
             data=res,type="l",lty=KEY$lines$lty,col=KEY$lines$col,
             key=KEY,
             xlab="Genotype Hazard Ratio",ylab="Power"))

# Illustrate Power (restricted to n=100)

print(xyplot(pow0~GHR|factor(erate),group=factor(raf),
             data=subset(res,n==ns[1]),
             type="l",lty=KEY$lines$lty,col=KEY$lines$col,
             key=KEY,
             xlab="Genotype Hazard Ratio",ylab="Power",
             sub=paste("n=",ns[1],", alpha=",round(unique(res$alpha),2))))

survSNP documentation built on Feb. 16, 2023, 10:10 p.m.