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missRows

Handling Missing Individuals in Multi-Omics Data Integration


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("missRows")):

Installation

To install this package, start R (version "4.3") 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")
missRows PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DimensionReduction, MathematicalBiology, PrincipalComponent, Software, StatisticalMethod, Visualization
Version 1.22.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License Artistic-2.0
Depends R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment
Imports plyr, stats, gtools, S4Vectors
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Suggests BiocStyle, knitr, testthat
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Package Archives

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

Source Package missRows_1.22.0.tar.gz
Windows Binary missRows_1.22.0.zip (64-bit only)
macOS Binary (x86_64) missRows_1.22.0.tgz
macOS Binary (arm64) missRows_1.22.0.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