imputeLCMD: A collection of methods for left-censored missing data imputation

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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.

Author
Cosmin Lazar
Date of publication
2015-01-19 07:09:10
Maintainer
Cosmin Lazar <vcosminlazar@gmail.com>
License
GPL (>= 2)
Version
2.0

View on CRAN

Man pages

generate.ExpressionData
Generate Peptide/Protein Expression Data
generate.RollUpMap
Generates peptide to protein map.
impute.MAR
Generic function for the imputation of MAR/MCAR missing data
impute.MAR.MNAR
Hybrid imputation method
impute.MinDet
Imputation of left-censored missing data using a...
impute.MinProb
Imputation of left-censored missing data using stochastic...
impute.QRILC
Imputation of left-censored missing data using QRILC method.
impute.wrapper.KNN
Wrapper function for KNN imputation.
impute.wrapper.MLE
MLE-based imputation of missing data.
impute.wrapper.SVD
SVD-based imputation.
impute.ZERO
Imputation of missing entries by '0'.
insertMVs
Generates missing data in a complete data matrix.
intensity_PXD000022
Dataset PXD000022 from ProteomeXchange.
intensity_PXD000052
Dataset PXD000052 from ProteomeXchange.
intensity_PXD000438
Dataset PXD000438 from ProteomeXchange.
intensity_PXD000501
Dataset PXD000501 from ProteomeXchange.
model.Selector
Model selector for hybrid missing data imputation
pep2prot
Peptide to protein mapping.

Files in this package

imputeLCMD
imputeLCMD/NAMESPACE
imputeLCMD/data
imputeLCMD/data/intensity_PXD000438.rda
imputeLCMD/data/intensity_PXD000022.rda
imputeLCMD/data/intensity_PXD000052.rda
imputeLCMD/data/intensity_PXD000501.rda
imputeLCMD/R
imputeLCMD/R/impMinProb.R
imputeLCMD/R/impZERO.R
imputeLCMD/R/imputeMAR-MNAR.R
imputeLCMD/R/imputeMAR.R
imputeLCMD/R/impKNN.R
imputeLCMD/R/impMLE.R
imputeLCMD/R/impMinDet.R
imputeLCMD/R/pep2protRollUp.R
imputeLCMD/R/generatePepData.R
imputeLCMD/R/modelSelector.R
imputeLCMD/R/generateRollUpMap.R
imputeLCMD/R/impQRILC.R
imputeLCMD/R/insertMVs.R
imputeLCMD/R/impSVD.R
imputeLCMD/MD5
imputeLCMD/DESCRIPTION
imputeLCMD/man
imputeLCMD/man/model.Selector.Rd
imputeLCMD/man/impute.wrapper.SVD.Rd
imputeLCMD/man/impute.MAR.Rd
imputeLCMD/man/impute.MinProb.Rd
imputeLCMD/man/impute.QRILC.Rd
imputeLCMD/man/intensity_PXD000501.Rd
imputeLCMD/man/generate.RollUpMap.Rd
imputeLCMD/man/intensity_PXD000052.Rd
imputeLCMD/man/impute.ZERO.Rd
imputeLCMD/man/impute.wrapper.MLE.Rd
imputeLCMD/man/intensity_PXD000022.Rd
imputeLCMD/man/insertMVs.Rd
imputeLCMD/man/impute.MAR.MNAR.Rd
imputeLCMD/man/pep2prot.Rd
imputeLCMD/man/impute.MinDet.Rd
imputeLCMD/man/impute.wrapper.KNN.Rd
imputeLCMD/man/generate.ExpressionData.Rd
imputeLCMD/man/intensity_PXD000438.Rd