missRows

DOI: 10.18129/B9.bioc.missRows  

Handling Missing Individuals in Multi-Omics Data Integration

Bioconductor version: Release (3.16)

The missRows package implements the MI-MFA method to deal with missing individuals ('biological units') in multi-omics data integration. The MI-MFA method generates multiple imputed datasets from a Multiple Factor Analysis model, then the yield results are combined in a single consensus solution. The package provides functions for estimating coordinates of individuals and variables, imputing missing individuals, and various diagnostic plots to inspect the pattern of missingness and visualize the uncertainty due to missing values.

Author: Ignacio Gonzalez and Valentin Voillet

Maintainer: Gonzalez Ignacio <ignacio.gonzalez at bbox.fr>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("missRows")

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("missRows")

 

PDF	R Script	missRows
PDF		Reference Manual
Text		NEWS

Details

biocViews	DimensionReduction, MathematicalBiology, PrincipalComponent, Software, StatisticalMethod, Visualization
Version	1.18.0
In Bioconductor since	BioC 3.7 (R-3.5) (5 years)
License	Artistic-2.0
Depends	R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment
Imports	plyr, stats, gtools, S4Vectors
LinkingTo
Suggests	BiocStyle, knitr, testthat
SystemRequirements
Enhances
URL
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	missRows_1.18.0.tar.gz
Windows Binary	missRows_1.18.0.zip
macOS Binary (x86_64)	missRows_1.18.0.tgz
macOS Binary (arm64)	missRows_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/missRows
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/missRows
Bioc Package Browser	https://code.bioconductor.org/browse/missRows/
Package Short Url	https://bioconductor.org/packages/missRows/
Package Downloads Report	Download Stats