Shrinkage-package: Several Shrinkage Estimators.
In Shrinkage: Several Shrinkage Effect-Size Estimators

Description Details Author(s) References See Also Examples

Several shrinkage estimators of the effect-size of a parameter of interest based on different criteria.

Package:	Shrinkage
Type:	Package
Version:	1.0
Date:	2015-10-20
License:	GPL-3
Depends:	methods, PsiHat, multtest, limma

Code: Corey M. Yanofsky, Zahra Montazeri, David R. Bickel and Marta Padilla
Documentation: Alaa Ali and Marta Padilla
Maintainer: M. Padilla <padilla.mpf@gmail.com>

Montazeri, Z., Yanofsky, C. M., & Bickel, D. R. (2010). Shrinkage estimation of effect sizes as an alternative to hypothesis testing followed by estimation in high-dimensional biology: applications to differential gene expression. Statistical applications in genetics and molecular biology, 9(1), Article 23.

Yanofsky, C. M., & Bickel, D. R. (2010). Validation of differential gene expression algorithms: Application comparing fold-change estimation to hypothesis testing. BMC Bioinformatics, 11, 63.

PsiHat, multtest and locfdr packages.

#simulate some data sets: matrices of log-abundance levels
nsam<-5         #number of individuals
nfeat<-6        #number of features (metabolites, genes,...)
diffs<-c(1,4)   #features with differential log-abundance levels
lfc<-5          #differential quantity

# create data sets:
x <- matrix(runif(nfeat*nsam), nrow = nfeat, ncol = nsam) #case
y <- matrix(runif(nfeat*nsam), nrow = nfeat, ncol = nsam) #control
x[diffs,] <- x[diffs,] + lfc

# Examples:

z1 <- nQ1.est(x=x,mu0=0.1,c=0.4)
z2 <- nQ2.est(x=x,y=y,a=0.4,b=0.02)
z3 <- nlocfdr.x(x=x,y=y)      
z4 <- nIC.est(x=x,opt="BF")

z5 <- nscottberger.est(x=x)
z6 <- other.est (x=x,y=y,opt="pseudo")
z7 <- nhard.threshold.est(x=x,y=y,alpha=1,opt="fc")