Package: msImpute 1.22.0

Soroor Hediyeh-zadeh

msImpute: Imputation of label-free mass spectrometry peptides

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).

Authors:Soroor Hediyeh-zadeh [aut, cre]

msImpute_1.22.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
msImpute/json (API)
NEWS

# Install 'msImpute' in R:
install.packages('msImpute', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/davislaboratory/msimpute/issues

Datasets:
  • pxd007959 - Processed peptide intensity matrix and experimental design table from PXD007959 study
  • pxd010943 - SWATH-MS Analysis of Gfi1-mutant bone marrow neutrophils
  • pxd014777 - Processed peptide intensity matrix from PXD014777 study

On BioConductor:msImpute-1.23.0(bioc 3.24)msImpute-1.22.0(bioc 3.23)

massspectrometryproteomicssoftwareimputation-algorithmlabel-free-proteomicslow-rank-approximation

5.32 score 15 stars 14 scripts 396 downloads 11 exports 77 dependencies

Last updated from:c3ac90e371 (on RELEASE_3_23). Checks:8 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING200
linux-devel-x86_64WARNING340
source / vignettesOK322
linux-release-x86_64WARNING354
macos-release-arm64WARNING211
macos-oldrel-arm64WARNING196
windows-develWARNING223
windows-releaseWARNING371
windows-oldrelWARNING260
wasm-releaseOK176

Exports:computeStructuralMetricsCPDevidenceToMatrixfindVariableFeaturesKNCKNNmsImputemspipplotCV2scaleDataselectFeatures

Dependencies:abindassortheadbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularblustercliclustercodetoolscpp11data.tableDelayedArraydplyrdqrngedgeRFNNformatRfutile.loggerfutile.optionsgenericsGenomicRangesgluehereigraphIRangesirlbajsonlitelambda.rlatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmetapodmvtnormpdistpillarpkgconfigpngpurrrR6rappdirsRcppRcppTOMLreticulaterlangrprojrootrsvdS4ArraysS4VectorsScaledMatrixscranscuttleSeqinfoSingleCellExperimentsitmosnowsoftImputeSparseArraystatmodstringistringrSummarizedExperimenttibbletidyrtidyselectutf8vctrswithrXVector

msImpute: Imputation of peptide intensity by low-rank approximation

Soroor Hediyeh-zadeh, Andrew I. Webb, Melissa J. Davis

Rendered frommsImpute-vignette.Rmdusingknitr::rmarkdownon Jun 08 2026.

Last update: 2020-10-20
Started: 2020-08-23