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 <[email protected]>

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.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ```
#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")
``` |

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