% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/FPRP.R
\name{FPRP}
\alias{FPRP}
\title{False-positive report probability}
\usage{
FPRP(a, b, pi0, ORlist, logscale = FALSE)
}
\arguments{
\item{a}{parameter value at which the power is to be evaluated.}

\item{b}{the variance for a, or the uppoer point of a 95\%CI if logscale=FALSE.}

\item{pi0}{the prior probabiility that \eqn{H_0}{H0} is true.}

\item{ORlist}{a vector of ORs that is most likely.}

\item{logscale}{FALSE=a,b in orginal scale, TRUE=a, b in log scale.}
}
\value{
The returned value is a list with compoents,
\describe{
\item{p}{p value corresponding to a,b}
\item{power}{the power corresponding to the vector of ORs}
\item{FPRP}{False-positive report probability}
\item{FNRP}{False-negative report probability}
}
}
\description{
The function calculates the false positive report probability (FPRP), the probability of no true
association beteween a genetic variant and disease given a statistically significant finding,
which depends not only on the observed P value but also on both the prior probability that the
assocition is real and the statistical power of the test. An associate result is the
false negative reported probability (FNRP).  See example for the recommended steps.
}
\details{
The FPRP and FNRP are derived as follows. Let \eqn{H_0}=null hypothesis (no association),
\eqn{H_A}=alternative hypothesis (association). Since classic frequentist theory considers 
they are fixed, one has to resort to Bayesian framework by introduing prior,
\eqn{\pi=P(H_0=TRUE)=P(association)}. Let \eqn{T}=test statistic, and \eqn{P(T>z_\alpha|H_0=TRUE)=P(rejecting\ 
H_0|H_0=TRUE)=\alpha}, \eqn{P(T>z_\alpha|H_0=FALSE)=P(rejecting\ H_0|H_A=TRUE)=1-\beta}. The joint
probability of test and truth of hypothesis can be expressed by \eqn{\alpha}, \eqn{\beta} and \eqn{\pi}.

\tabular{llll}{
%\multicolumn{4}{c}{Joint probability of significance of test and truth of hypothesis}\cr
%\tab \multicolumn{2}{c}{significance of test} \\ \cline{2-3}
Truth of \eqn{H_A} \tab significant \tab nonsignificant \tab Total\cr 
TRUE \tab \eqn{(1-\beta)\pi} \tab \eqn{\beta\pi} \tab \eqn{\pi}\cr
FALSE \tab \eqn{\alpha (1-\pi)} \tab \eqn{(1-\alpha)(1-\pi)} \tab \eqn{1-\pi}\cr
Total \tab \eqn{(1-\beta)\pi+\alpha (1-\pi)} \tab \eqn{\beta\pi+(1-\alpha)(1-\pi)} \tab 1\cr
}

We have \eqn{FPRP=P(H_0=TRUE|T>z_\alpha)= 
\alpha(1-\pi)/[\alpha(1-\pi)+(1-\beta)\pi]=\{1+\pi/(1-\pi)][(1-\beta)/\alpha]\}^{-1}}
and similarly \eqn{FNRP=\{1+[(1-\alpha)/\beta][(1-\pi)/\pi]\}^{-1}}.
}
\examples{
\dontrun{
# Example by Laure El ghormli & Sholom Wacholder on 25-Feb-2004
# Step 1 - Pre-set an FPRP-level criterion for noteworthiness

T <- 0.2

# Step 2 - Enter values for the prior that there is an association

pi0 <- c(0.25,0.1,0.01,0.001,0.0001,0.00001)

# Step 3 - Enter values of odds ratios (OR) that are most likely, assuming that
#          there is a non-null association

ORlist <- c(1.2,1.5,2.0)

# Step 4 - Enter OR estimate and 95\% confidence interval (CI) to obtain FPRP 												

OR <- 1.316
ORlo <- 1.08
ORhi <- 1.60

logOR <- log(OR)
selogOR <- abs(logOR-log(ORhi))/1.96
p <- ifelse(logOR>0,2*(1-pnorm(logOR/selogOR)),2*pnorm(logOR/selogOR))
p
q <- qnorm(1-p/2)
POWER <- ifelse(log(ORlist)>0,1-pnorm(q-log(ORlist)/selogOR),
                pnorm(-q-log(ORlist)/selogOR))
POWER
FPRPex <- t(p*(1-pi0)/(p*(1-pi0)+POWER\\%o\\%pi0))
row.names(FPRPex) <- pi0
colnames(FPRPex) <- ORlist
FPRPex
FPRPex>T

## now turn to FPRP
OR <- 1.316
ORhi <- 1.60
ORlist <- c(1.2,1.5,2.0)
pi0 <- c(0.25,0.1,0.01,0.001,0.0001,0.00001)
z <- FPRP(OR,ORhi,pi0,ORlist,logscale=FALSE)
z
}

}
\references{
Wacholder S, Chanock S, Garcia-Closas M, El ghomli L, Rothman N. (2004) Assessing the probability that a positive
report is false: an approach for molecular epidemiology studies. J Natl Cancer Inst 96:434-442
}
\seealso{
\code{\link[gap]{BFDP}}
}
\author{
Jing Hua Zhao
}
\keyword{models}