SHIP: SHrinkage covariance Incorporating Prior knowledge

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.

Author
Monika Jelizarow and Vincent Guillemot
Date of publication
2013-12-23 15:17:34
Maintainer
Vincent Guillemot <vincent.j.guillemot@gmail.com>
License
GPL (>= 2)
Version
1.0.2

View on CRAN

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.

Files in this package

SHIP
SHIP/NAMESPACE
SHIP/data
SHIP/data/expl.rda
SHIP/R
SHIP/R/check.path.R
SHIP/R/shrink.estim.R
SHIP/R/targetD.R
SHIP/R/targetGpos.R
SHIP/R/target.help.R
SHIP/R/build.target.R
SHIP/R/targetCor.R
SHIP/R/targetGstar.R
SHIP/R/targetG.R
SHIP/R/targetF.R
SHIP/MD5
SHIP/DESCRIPTION
SHIP/man
SHIP/man/build.target.Rd
SHIP/man/targetF.Rd
SHIP/man/check.path.Rd
SHIP/man/targetG.Rd
SHIP/man/targetD.Rd
SHIP/man/expl.Rd
SHIP/man/targetCor.Rd
SHIP/man/targetGpos.Rd
SHIP/man/targetGstar.Rd
SHIP/man/target.help.Rd
SHIP/man/SHIP-package.Rd
SHIP/man/shrink.estim.Rd