RLassoCox

DOI: 10.18129/B9.bioc.RLassoCox    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see RLassoCox.

A reweighted Lasso-Cox by integrating gene interaction information

Bioconductor version: 3.13

RLassoCox is a package that implements the RLasso-Cox model proposed by Wei Liu. The RLasso-Cox model integrates gene interaction information into the Lasso-Cox model for accurate survival prediction and survival biomarker discovery. It is based on the hypothesis that topologically important genes in the gene interaction network tend to have stable expression changes. The RLasso-Cox model uses random walk to evaluate the topological weight of genes, and then highlights topologically important genes to improve the generalization ability of the Lasso-Cox model. The RLasso-Cox model has the advantage of identifying small gene sets with high prognostic performance on independent datasets, which may play an important role in identifying robust survival biomarkers for various cancer types.

Author: Wei Liu [cre, aut]

Maintainer: Wei Liu <freelw at qq.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RLassoCox")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RLassoCox")

 

PDF	R Script	RLassoCox
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, GenePrediction, Network, Regression, Software, Survival
Version	1.0.0
In Bioconductor since	BioC 3.13 (R-4.1) (< 6 months)
License	Artistic-2.0
Depends	R (>= 4.1), glmnet
Imports	Matrix, igraph, survival, stats
LinkingTo
Suggests	knitr
SystemRequirements
Enhances
URL
BugReports	https://github.com/weiliu123/RLassoCox/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	RLassoCox_1.0.0.tar.gz
Windows Binary	RLassoCox_1.0.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	RLassoCox_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RLassoCox
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RLassoCox
Package Short Url	https://bioconductor.org/packages/RLassoCox/
Package Downloads Report	Download Stats