Package:
imputeLCMD
Authors:
Samuel Wieczorek, Thomas Burger, Cosmin Lazar
Category:
Left-Censored Missing Data
Use-Cases:
Left-censored data imputation, gene expression data generation
Popularity:
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.
Algorithms for imputation:
- impute.MAR() – Imputation under MAR/MCAR assumption,
- impute.MAR.MNAR() – Imputation under combined MCAR and MNAR assumption,
- impute.MinDet() – Imputation with minimum detection value,
- impute.MinProb() – Imputation using random draws from a left-censored distribution,
- impute.QRILC() – Imputation based on quantile regression for left-censored data,
- impute.wrapper.KNN() – Imputation using k-nearest neighbors,
- impute.wrapper.MLE() – Imputation using the EM algorithm (Maximum Likelihood Estimation),
- impute.wrapper.SVD() – Imputation based on Singular Value Decomposition,
- impute.ZERO() – Imputation by zero.
Algorithms for amputation:
- insertMVs() – Generate missing values in the dataset.
Datasets:
The artificial data can be generated using:
- generate.ExpressionData() - Generate expression data,
- generate.RollUpMap() – Generate roll-up map.
The datasets can be loaded using functions:
- intensity_PXD000022() – Load dataset PXD000022 from ProteomeXchange,
- intensity_PXD000052() – Load dataset PXD000052 from ProteomeXchange,
- intensity_PXD000438() – Load dataset PXD000438 from ProteomeXchange,
- intensity_PXD000501() – Load dataset PXD000501 from ProteomeXchange.
Further Information:
- Documentation: https://rdrr.io/cran/imputeLCMD/man/
Input:
data.frame, tibble
Example:
You can find a nice vignette with example usage here