msImpute

DOI: 10.18129/B9.bioc.msImpute    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see msImpute.

Imputation of label-free mass spectrometry peptides

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	msImpute: proteomics missing values imputation and diagnosis
PDF		Reference Manual
Text		NEWS

Details

biocViews	MassSpectrometry, Proteomics, Software
Version	1.6.0
In Bioconductor since	BioC 3.12 (R-4.0) (2 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
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD
SystemRequirements	python
Enhances
URL
BugReports	https://github.com/DavisLaboratory/msImpute/issues
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	msImpute_1.6.0.tar.gz
Windows Binary	msImpute_1.6.0.zip
macOS Binary (x86_64)	msImpute_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/msImpute
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/msImpute
Package Short Url	https://bioconductor.org/packages/msImpute/
Package Downloads Report	Download Stats