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imputeLCMD (version 2.0)

A collection of methods for left-censored missing data imputation

Description

The package contains a collection of functions for left-censored missing data imputation. Left-censoring is a special case of missing not at random (MNAR) mechanism that generates non-responses in proteomics experiments. The package also contains functions to artificially generate peptide/protein expression data (log-transformed) as random draws from a multivariate Gaussian distribution as well as a function to generate missing data (both randomly and non-randomly). For comparison reasons, the package also contains several wrapper functions for the imputation of non-responses that are missing at random. * New functionality has been added: a hybrid method that allows the imputation of missing values in a more complex scenario where the missing data are both MAR and MNAR.

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Version

Install

install.packages('imputeLCMD')

Monthly Downloads

1,497

Version

2.0

License

GPL (>= 2)

Maintainer

Last Published

January 19th, 2015

Functions in imputeLCMD (2.0)

generate.RollUpMap

Generates peptide to protein map.
impute.MinProb

Imputation of left-censored missing data using stochastic minimal value approach.
impute.QRILC

Imputation of left-censored missing data using QRILC method.
impute.wrapper.SVD

SVD-based imputation.
pep2prot

Peptide to protein mapping.
generate.ExpressionData

Generate Peptide/Protein Expression Data
intensity_PXD000022

Dataset PXD000022 from ProteomeXchange.
impute.ZERO

Imputation of missing entries by 0.
impute.MAR

Generic function for the imputation of MAR/MCAR missing data
intensity_PXD000052

Dataset PXD000052 from ProteomeXchange.
model.Selector

Model selector for hybrid missing data imputation
intensity_PXD000438

Dataset PXD000438 from ProteomeXchange.
impute.MinDet

Imputation of left-censored missing data using a deterministic minimal value approach.
impute.wrapper.MLE

MLE-based imputation of missing data.
insertMVs

Generates missing data in a complete data matrix.
intensity_PXD000501

Dataset PXD000501 from ProteomeXchange.
impute.MAR.MNAR

Hybrid imputation method
impute.wrapper.KNN

Wrapper function for KNN imputation.