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msImpute

Imputation of label-free mass spectrometry peptides


Bioconductor version: Release (3.18)

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 (from within R, enter citation("msImpute")):

Installation

To install this package, start R (version "4.3") and enter:


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

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 PDF
NEWS Text

Details

biocViews MassSpectrometry, Proteomics, Software
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 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
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Suggests BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD
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Package Archives

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

Source Package msImpute_1.12.0.tar.gz
Windows Binary msImpute_1.12.0.zip (64-bit only)
macOS Binary (x86_64) msImpute_1.12.0.tgz
macOS Binary (arm64) msImpute_1.12.0.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