SHIP: SHrinkage covariance Incorporating Prior knowledge
Version 1.0.2

The SHIP-package allows the estimation of various types of shrinkage covariance matrices. These types differ in terms of the so-called covariance target (to be chosen by the user), the highly structured matrix which the standard unbiased sample covariance matrix is shrunken towards and which optionally incorporates prior biological knowledge extracted from the database KEGG. The shrinkage intensity is obtained via an analytical procedure.

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AuthorMonika Jelizarow and Vincent Guillemot
Date of publication2013-12-23 15:17:34
MaintainerVincent Guillemot <vincent.j.guillemot@gmail.com>
LicenseGPL (>= 2)
Version1.0.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("SHIP")

Man pages

build.target: Creating a covariance target, optionally by using information...
check.path: Check if two genes belong to any common KEGG pathway.
expl: Small example extracted from a microarray data set.
SHIP-package: SHrinkage covariance Incorporating Prior knowledge
shrink.estim: Shrinkage estimator of the covariance matrix, given a data...
targetCor: Computation of the target Cor.
targetD: Computation of the diagonal target D ('diagonal, unequal...
targetF: Computation of target F ('constant correlation model').
targetG: Computation of target G ('knowledge-based constant...
targetGpos: Computation of the target Gpos.
targetGstar: Computation of the target Gstar.
target.help: Transform a list of Pathway IDs into a binary matrix.

Functions

SHIP-package Man page
build.target Man page Source code
check.path Man page Source code
expl Man page
shrink.estim Man page Source code
target.help Man page Source code
targetCor Man page Source code
targetD Man page Source code
targetF Man page Source code
targetG Man page Source code
targetGpos Man page Source code
targetGstar Man page Source code

Files

NAMESPACE
data
data/expl.rda
R
R/check.path.R
R/shrink.estim.R
R/targetD.R
R/targetGpos.R
R/target.help.R
R/build.target.R
R/targetCor.R
R/targetGstar.R
R/targetG.R
R/targetF.R
MD5
DESCRIPTION
man
man/build.target.Rd
man/targetF.Rd
man/check.path.Rd
man/targetG.Rd
man/targetD.Rd
man/expl.Rd
man/targetCor.Rd
man/targetGpos.Rd
man/targetGstar.Rd
man/target.help.Rd
man/SHIP-package.Rd
man/shrink.estim.Rd
SHIP documentation built on May 29, 2017, 11:25 a.m.