mlm4omics

DOI: 10.18129/B9.bioc.mlm4omics    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see mlm4omics.

Multilevel Model for Multivariate Responses with Missing Values

Bioconductor version: 3.8

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 "3.5") 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

PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, Classification, CopyNumberVariation, ImmunoOncology, MassSpectrometry, Proteomics, Regression, Software
Version	1.0.1
In Bioconductor since	BioC 3.8 (R-3.5) (0.5 years)
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
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Package Archives

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

Source Package
Windows Binary	mlm4omics_1.0.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)
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	http://bioconductor.org/packages/mlm4omics/
Package Downloads Report	Download Stats