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imputomics

imputomics is an R package and a shiny web server designed to simulate and impute missing values. It offers 42 algorithms for imputing missing values, especially in different types of ‘-omics’ data such as genomics, transcriptomics, proteomics, and metabolomics. imputomics provides a user-friendly interface that allows users to simulate missing values based on different distributions and impute missing values using state-of-the-art methods.

Key Features:

  1. Imputation methods: imputomics offers the biggest collection of imputation methods for different types of omics data, including k-nearest neighbors (KNN), random forests, expectation-maximization (EM) algorithm, and principal components analysis (PCA) and many others.

  2. Performance evaluation: imputomics facilitates evaluating the performance of imputation methods. Users can evaluate imputation accuracy and compare different methods using metrics such as root mean squared error (RMSE), mean absolute error (MAE), and coefficient of determination (R-squared).

  3. Simulation of missing values: imputomics provides a variety of options for simulating missing values, including missing completely at random (MCAR), missing at random (MAR), and missing not at random (MNAR) mechanisms. Users can specify the percentage of missing values and the distribution from which the missing values are generated.

Getting started

This repository contains the data and code necessary to reproduce the results from the paper imputomics: comprehensive missing data imputation for metabolomics data. It uses renv package to assure the reproducibility. As imputomics implements lots of missing value imputations methods from other R packages.

Webserver

The imputomics can be accessed through our web server.

Installation

imputomics is available on GitHub

To install imputomics you need to have R version >= 4.2.0.

devtools::install_github("BioGenies/imputomics")

Sometimes, not all packages can be installed on the first try. In this case, consider re-running the install_github function.

Docker

To enhance the reproducibility of imputomics, we share it also as a rocker-based container. The docker manifest is available in the imputomics repository: https://github.com/BioGenies/imputomics/blob/main/Dockerfile_imputomics.

Reproducibility

To reproduce our environment you need to git clone our repo and activate renv.

git clone https://github.com/BioGenies/imputomics.git
renv::activate()
renv::restore()

Troubleshooting

Q: I am receiving the following error message: “Error: HTTP error 403. API rate limit exceeded for [my IP]”. A: Due to its comprehensiveness, imputomics downloads many packages from GitHub, which may lead to exceeding the limit of GitHub API queries. Please consider setting the GitHub API token with usethis::create_github_token().

Run imputomics

To run imputomics type the following command into an R console.

imputomics::imputomics_gui()

How to cite?

Jarosław Chilimoniuk, Krystyna Grzesiak, Jakub Kała, Dominik Nowakowski, Adam Krętowski, Rafał Kolenda, Michał Ciborowski, Michał Burdukiewicz (2023). imputomics: web server and R package for missing values imputation in metabolomics data, Bioinformatics, 10.1093/bioinformatics/btae098.

Contact

If you have any questions, suggestions or comments, contact Michal Burdukiewicz.

Funding and acknowledgements

We want to thank the Clinical Research Centre (Medical University of Białystok) members for fruitful discussions. K.G. wants to acknowledge grant no. 2021/43/O/ST6/02805 (National Science Centre). M.C. acknowledges grant no. B.SUB.23.533 (Medical University of Białystok). The study was supported by the Ministry of Education and Science funds within the project ‘Excellence Initiative - Research University’. We also acknowledge the Center for Artificial Intelligence at the Medical University of Białystok (funded by the Ministry of Health of the Republic of Poland).