proteomicdesign (version 2.0)

power.single.cost: Derive the averaged estimated costs of stage II and III and the stage III sample size from the 1000 Monte Carlo simulated functions of a three-stage proteomic study, given a solution of the design parameters

Description

The power.single.cost estimated the average costs at stage II and III and derive the stage III sample size with a user defined solution from the optim.two.stage.single() To obtain the cost and stage III sample size, the parameter "optimize" need to set to the default value "FALSE". Otherwise, it will give the expected number of proteins with true effect instead.

Usage

power.single.cost(initial, protein, n1, artifact, budget, s, assaycost2.function, assaycost3.function, recruit, optimize = FALSE)

Arguments

initial

, A vector of the solution from the optim.two.stage.single(), it comprises of stage I/II t test p value thresholds, and stage II sample size

protein

The protein dataset that needs to have three variables: proteinid, beta, sigma. proteinid is the numerical id for each protein, beta is the mean difference, sigma is the standard deviation of the difference. The protein dataset need to have at least 2 p

n1

The stage I sample size

artifact

The technical artifact correction factor for each protein

budget

The budget of the three-stage proteomic study for the stage II verification and stage III clinical validation: it does not include stage I cost

s

The slake term of the total budget which is a small amount of dollars that transfers the inequality constraint to an equal constraint. The default value is 1000 dollars.

assaycost2.function

The assay cost function of number of proteins (p) and number of patients(n) at stage II.

assaycost3.function

The assay cost function of number of proteins (p) ONLY at stage III.

recruit

The recruitment cost for a patient assuming it is the same at each stage. The default value is 100.

optimize

A logical variable, the default value is FALSE when it will output stage III sample size, the costs for stage II and III. When the value sets to TRUE, it will output the expected number of detected proteins with true effect for the defined solution.

Value

• mean.n3
  The averaged stage III sample size
• mean.stage2.cost
  The averaged stage II cost
• mean.stage3.cost
  The averaged stage III cost

See Also

power.group.cost(), optim.two.stage.single(), optim.two.stage.group(),optim.two.stage.appr()

Examples

assaycost2=function(n,p){280*p+1015*n}
assaycost3=function(p){200*p}
protein<-data.frame(proteinid=c(100,101,103,104,105),beta=c(2.4,2.6,0.5,2.6,0.7),sigma=c(0.6,0.7,0.3,0.7,0.4),group=c(1,1,1,2,2))
initial=c(0.01,0.01,100)
power.single.cost(initial,protein=protein,artifact=rep(1,5),n1=30,budget=500000,s=1000,assaycost2.function=assaycost2,assaycost3.function=assaycost3,recruit=100,optimize=FALSE)