Learn R Programming

imputeLCMD (version 2.1)

A Collection of Methods for Left-Censored Missing Data Imputation

Description

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.

Copy Link

Version

Install

install.packages('imputeLCMD')

Monthly Downloads

1,497

Version

2.1

License

GPL (>= 2)

Last Published

June 10th, 2022

Functions in imputeLCMD (2.1)

model.Selector

Identifies row in the data matrix affected by a MNAR missingness mechanism
intensity_PXD000022

Dataset PXD000022 from ProteomeXchange.
impute.MAR

imputation under MAR/MCAR hypothesis
intensity_PXD000052

Dataset PXD000052 from ProteomeXchange.
intensity_PXD000501

Dataset PXD000501 from ProteomeXchange.
intensity_PXD000438

Dataset PXD000438 from ProteomeXchange.
pep2prot

peptide to protein roll-up
impute.wrapper.SVD

imputation based on SVD algorithm
insertMVs

Generates missing values in data.
impute.ZERO

Imputation by 0.
impute.wrapper.MLE

imputation using the EM algorithm
generate.RollUpMap

Generate roll up map
impute.MinDet

Imputation with min value
impute.MinProb

Imputation by random draws
impute.MAR.MNAR

Imputation under MCAR and MNAR hypothesis
impute.wrapper.KNN

Imputation with KNN
impute.QRILC

imputation based on quantile regression
generate.ExpressionData

Generate expression data