CorrectedFDR (version 1.1)

BlendedLFDR: Blended Estimator of Local False Discovery Rate (LFDR)

Description

BlendedLFDR is a function used to compute the blended estimator based on a benchmark estimator, usually the nonlocal false discovery rate (NFDR), and a set of estimators of local false discovery rates (LFDR).

Usage

BlendedLFDR(Benchmark, EstLFDR)

Arguments

Benchmark

Input numeric vector for benchmark estimator (often NFDR).

EstLFDR

Input a matrix containing two or more sets of LFDR estimators.

Value

The value of the blended estimator is an estimator of the LFDR.

Details

Benchmark is an estimator of the FDR. This is usually the nonlocal false discovery rate (NFDR). EstLFDR is a matrix of several LFDR estimators such as corrected FDR (CFDR), re-ranked FDR (RFDR), MLE (Maximum Likelihood Estimator), BBE1(Binomial Based Estimator), etc. The output returns a single numeric vector containing the blended estimator of the LFDR.

References

Bickel, D. R. (2015). Blending Bayesian and frequentist methods according to the precision of prior information with applications to hypothesis testing. Statistical Methods and Applications, 24(4), pp. 523-546.

Examples

# NOT RUN {
#The data used to compute the LFDR estimators (CFDR, RFDR, MLE, and BBE1)
#comes from the ER/PR breast cancer data from the "ProData" package.
#To read more about the data, visit the website: https://www.bioconductor.org/
#Test statistics were first obtain, then the estimators for the FDR and LFDR were estimated.
#Benchmark vector
NFDR<-c(0.5661106448, 0.6897735492, 0.0000288516, 0.1549745113, 0.1305508970, 0.2421032979,
0.1482335568, 1, 1, 1, 0.6602562820, 0.7034682859, 0.7036332234, 0.0071192090,
0.8204536037, 0.9757716498, 0.7379329991, 1, 0.6333245479, 0.9904389701)
#Estimators of LFDR
CFDR<- c(1, 1, 0.0000288516, 0.2841199373, 0.2980912149, 0.5931530799, 0.3088199101,
1, 1, 1, 1, 1, 1, 0.0106788135, 1, 1, 1, 1, 1, 1)

RFDR<- c(0.689773549, 1, 0.007119209, 0.130550897, 0.703633223, 0.660256282, 0.242103298,
1, 1, 1, 0.820453604, 1, 0.703468286, 0.154974511, 1, 1, 1, 1, 0.975771650,1)

MLE<- c(0.9865479126, 0.9969935995, 0.0002372158, 0.6531633437, 0.7611453549, 0.9187425383,
0.7359259207, 0.9996548155, 0.9997310453, 0.9997437131, 0.9944712582, 0.9981685029,
0.9937604664, 0.0215892618, 0.9990504315, 0.9997493086, 0.9967673540, 0.9997016985,
0.9970142319, 0.9997625673)

BBE1<- c(1,1, 0.0003169812, 0.1138333734, 1, 1, 1, 1, 1, 1, 0.3279109564, 1, 0.0504755806,
0.0091823115, 0.0182614994, 0.0165386682, 1, 0.6964403713, 0.1001337298, 0.8415641198 )

#Matrix of LFDR Estimators
Est.LFDR<- matrix(c(CFDR,RFDR,MLE,BBE1), ncol=4)
output<-BlendedLFDR(Benchmark = NFDR, EstLFDR = Est.LFDR)
output$Blended
# }