mlm4omics

DOI: 10.18129/B9.bioc.mlm4omics    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see mlm4omics.

Multilevel Model for Multivariate Responses with Missing Values

Bioconductor version: 3.9

To conduct Bayesian inference regression for responses with multilevel explanatory variables and missing values; It uses function from 'Stan', a software to implement posterior sampling using Hamiltonian MC and its variation Non-U-Turn algorithms. It implements the posterior sampling of regression coefficients from the multilevel regression models. The package has two main functions to handle not-missing-at-random missing responses and left-censored with not-missing-at random responses. The purpose is to provide a similar format as the other R regression functions but using 'Stan' models.

Author: Irene Zeng [aut, cre], Thomas Lumley [ctb]

Maintainer: Irene SL Zeng <i.zeng at auckland.ac.nz>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("mlm4omics")

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("mlm4omics")

 

HTML	R Script	Introduction of mlm4omics
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, Classification, CopyNumberVariation, ImmunoOncology, MassSpectrometry, Proteomics, Regression, Software
Version	1.2.0
In Bioconductor since	BioC 3.8 (R-3.5) (1 year)
License	GPL-3
Depends	R (>= 3.5.0), Rcpp (>= 0.12.17), methods, stats
Imports	rstan (>= 2.17.3), rstantools (>= 1.5.0), MASS, Matrix, stats4, ggplot2
LinkingTo	StanHeaders (>= 2.17.2), rstan (>= 2.17.3), BH (>= 1.66.0-1), Rcpp (>= 0.12.17), RcppEigen (>= 0.3.3.4.0)
Suggests	testthat, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0)
SystemRequirements	GNU make
Enhances
URL	https://doi.org/10.1101/153049
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	mlm4omics_1.2.0.tar.gz
Windows Binary	mlm4omics_1.2.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	mlm4omics_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mlm4omics
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mlm4omics
Package Short Url	https://bioconductor.org/packages/mlm4omics/
Package Downloads Report	Download Stats