missRows
This is the development version of missRows; for the stable release version, see missRows.
Handling Missing Individuals in Multi-Omics Data Integration
Bioconductor version: Development (3.24)
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("missRows")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DimensionReduction, MathematicalBiology, PrincipalComponent, Software, StatisticalMethod, Visualization |
| Version | 1.33.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (8.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment |
| Imports | plyr, stats, gtools, S4Vectors |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, testthat |
| 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 | missRows_1.33.0.tar.gz |
| Windows Binary (x86_64) | missRows_1.33.0.zip |
| macOS Binary (big-sur-x86_64) | missRows_1.33.0.tgz |
| macOS Binary (sonoma-arm64) | missRows_1.33.0.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 |