SHIP: Shrinkage Covariance Estimation with Prior Knowledge

Package: SHIP 2.1.0

Vincent Guillemot

SHIP: Shrinkage Covariance Estimation with Prior Knowledge

Estimates shrinkage covariance matrices from data using user-selected targets, including diagonal, constant-correlation, and knowledge-based targets informed by functional gene groups. The shrinkage intensity is computed analytically.

Authors:Vincent Guillemot [aut, cre], Monika Jelizarow [aut]

SHIP_2.1.0.tar.gz
SHIP_2.1.0.zip(r-4.7-any)SHIP_2.1.0.zip(r-4.6-any)SHIP_2.1.0.zip(r-4.5-any)
SHIP_2.1.0.tgz(r-4.6-any)SHIP_2.1.0.tgz(r-4.5-any)
SHIP_2.1.0.tar.gz(r-4.7-any)SHIP_2.1.0.tar.gz(r-4.6-any)
SHIP_2.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SHIP/json (API)

# Install 'SHIP' in R:

install.packages('SHIP', repos = c('https://vguillemot.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/vguillemot/ship/issues

Datasets:

expl - Small example extracted from a microarray data set.

On CRAN:

quarto

4.93 score 17 scripts 212 downloads 11 mentions 10 exports 0 dependencies

Last updated from:821aa31dc9. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	122
source / vignettes	OK	166
linux-release	OK	116
macos-release	OK	223
macos-oldrel	OK	215
windows-devel	OK	96
windows-release	OK	108
windows-oldrel	OK	144
wasm-release	OK	79

Exports:build.target check.path shrink.estim target.help targetCor targetD targetF targetG targetGpos targetGstar

Dependencies:

A short introduction to SHIP

The example data | Comparing covariance targets | Estimating a covariance matrix

Rendered fromship-overview.qmdusingquarto::html

Help page	Topics
SHIP provides shrinkage covariance estimation with user-selected targets. The available targets include diagonal, constant-correlation, and knowledge-based structures informed by functional gene groups.	SHIP-package SHIP
Creating a covariance target, optionally by using information from KEGG pathways.	build.target
Check if two genes belong to any common KEGG pathway.	check.path
Small example extracted from a microarray data set.	expl
Shrinkage estimator of the covariance matrix, given a data set and a covariance target.	shrink.estim
Transform a list of Pathway IDs into a binary matrix.	target.help
Significance-filtered knowledge-based target.	targetCor
Diagonal covariance target.	targetD
Constant-correlation covariance target.	targetF
Knowledge-based constant-correlation target.	targetG
Positive-correlation knowledge-based target.	targetGpos
Signed-correlation knowledge-based target.	targetGstar

Help page

Topics

SHIP provides shrinkage covariance estimation with user-selected targets. The available targets include diagonal, constant-correlation, and knowledge-based structures informed by functional gene groups.

SHIP-package SHIP

Creating a covariance target, optionally by using information from KEGG pathways.

build.target

Check if two genes belong to any common KEGG pathway.

check.path

Small example extracted from a microarray data set.

expl

Shrinkage estimator of the covariance matrix, given a data set and a covariance target.

shrink.estim