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 (3.21)
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] (ORCID:
Maintainer: Soroor Hediyeh-zadeh <hediyehzadeh.s at wehi.edu.au>
citation("msImpute")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 | 1.17.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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_1.17.0.tar.gz |
| Windows Binary (x86_64) | msImpute_1.17.0.zip (64-bit only) |
| macOS Binary (x86_64) | msImpute_1.17.0.tgz |
| macOS Binary (arm64) | |
| 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 |