Imputation of label-free mass spectrometry peptides

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Documentation for package ‘msImpute’ version 1.19.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

computeStructuralMetrics	Metrics for the assessment of post-imputation structural preservation
CPD	CPD
evidenceToMatrix	Creates intensity matrix from tabular data in evidence table of MaxQuant
findVariableFeatures	Find highly variable peptides
KNC	k-nearest class means (KNC)
KNN	k-nearest neighbour (KNN)
msImpute	Imputation of peptide log-intensity in mass spectrometry label-free proteomics by low-rank approximation
mspip	Fills missing values by Peptide Identity Propagation (PIP)
plotCV2	Plot mean-CV^2 trend
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
scaleData	Standardize a matrix to have optionally row means zero and variances one, and/or column means zero and variances one.
selectFeatures	Select features for MAR/MNAR pattern examination