sparsenetgls
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see sparsenetgls.
Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression
Bioconductor version: 3.9
The package provides methods of combining the graph structure learning and generalized least squares regression to improve the regression estimation. The main function sparsenetgls() provides solutions for multivariate regression with Gaussian distributed dependant variables and explanatory variables utlizing multiple well-known graph structure learning approaches to estimating the precision matrix, and uses a penalized variance covariance matrix with a distance tuning parameter of the graph structure in deriving the sandwich estimators in generalized least squares (gls) regression. This package also provides functions for assessing a Gaussian graphical model which uses the penalized approach. It uses Receiver Operative Characteristics curve as a visualization tool in the assessment.
Author: Irene Zeng [aut, cre], Thomas Lumley [ctb]
Maintainer: Irene Zeng <i.zeng at auckland.ac.nz>
citation("sparsenetgls")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sparsenetgls")
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("sparsenetgls")| Introduction to sparsenetgls | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, GraphAndNetwork, ImmunoOncology, MassSpectrometry, Metabolomics, Proteomics, Regression, Software, Visualization |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0), Matrix, MASS |
| Imports | methods, glmnet, parcor, huge, stats, graphics, utils |
| System Requirements | GNU make |
| URL |
See More
| Suggests | testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | sparsenetgls_1.2.0.tar.gz |
| Windows Binary | sparsenetgls_1.2.0.zip |
| Mac OS X 10.11 (El Capitan) | sparsenetgls_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/sparsenetgls |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/sparsenetgls |
| Bioc Package Browser | https://code.bioconductor.org/browse/sparsenetgls/ |
| Package Short Url | https://bioconductor.org/packages/sparsenetgls/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |