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 <email@example.com>|
|License||GPL (>= 2)|
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.