msImpute
This is the development version of msImpute; for the stable release version, see msImpute.
Imputation of label-free mass spectrometry peptides
Bioconductor version: Development (3.24)
MsImpute is a package for imputation of peptide intensity in proteomics experiments. It additionally contains tools for MAR/MNAR diagnosis and assessment of distortions to the probability distribution of the data post imputation. The missing values are imputed by low-rank approximation of the underlying data matrix if they are MAR (method = "v2"), by Barycenter approach if missingness is MNAR ("v2-mnar"), or by Peptide Identity Propagation (PIP).
Author: Soroor Hediyeh-zadeh [aut, cre]
Maintainer: Soroor Hediyeh-zadeh <hediyehzadeh.s at wehi.edu.au>
citation("msImpute")):
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("msImpute")
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("msImpute")| msImpute: proteomics missing values imputation and diagnosis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | MassSpectrometry, Proteomics, Software |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | GPL (>=2) |
| Depends | R (>= 3.5.0) |
| Imports | softImpute, methods, stats, graphics, pdist, reticulate, scran, data.table, FNN, matrixStats, limma, mvtnorm, tidyr, dplyr |
| System Requirements | python |
| URL | |
| Bug Reports | https://github.com/DavisLaboratory/msImpute/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD |
| 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 | msImpute_1.23.0.tar.gz |
| Windows Binary (x86_64) | msImpute_1.23.0.zip |
| macOS Binary (big-sur-x86_64) | msImpute_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | msImpute_1.23.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/msImpute |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/msImpute |
| Bioc Package Browser | https://code.bioconductor.org/browse/msImpute/ |
| Package Short Url | https://bioconductor.org/packages/msImpute/ |
| Package Downloads Report | Download Stats |