Package: BEclear 2.23.0

Livia Rasp

BEclear: Correction of batch effects in DNA methylation data

Provides functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.

Authors:Livia Rasp [aut, cre], Markus Merl [aut], Ruslan Akulenko [aut]

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BEclear.pdf |BEclear.html✨
BEclear/json (API)
NEWS

# Install 'BEclear' in R:
install.packages('BEclear', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/uds-helms/beclear/issues10 issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • ex.corrected.data - Example matrix of corrected data for the BEclear-package
  • ex.data - Example data set for the BEclear-package
  • ex.samples - Example data set for the BEclear-package

On BioConductor:BEclear-2.23.0(bioc 3.21)BEclear-2.22.0(bioc 3.20)

batcheffectdnamethylationsoftwarepreprocessingstatisticalmethodbatch-effectsbioconductor-packagedna-methylationlatent-factor-modelmethylationmissing-datamissing-valuesstochastic-gradient-descentcpp

5.90 score 4 stars 11 scripts 372 downloads 3 mentions 13 exports 22 dependencies

Last updated 5 months agofrom:4a3e2f429e. Checks:1 OK, 10 NOTE, 1 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 29 2025
R-4.5-win-x86_64NOTEMar 29 2025
R-4.5-mac-x86_64NOTEMar 29 2025
R-4.5-mac-aarch64NOTEMar 29 2025
R-4.5-linux-x86_64NOTEMar 29 2025
R-4.4-win-x86_64NOTEMar 29 2025
R-4.4-mac-x86_64NOTEMar 29 2025
R-4.4-mac-aarch64NOTEMar 29 2025
R-4.4-linux-x86_64NOTEMar 29 2025
R-4.3-win-x86_64NOTEMar 29 2025
R-4.3-mac-x86_64NOTEMar 29 2025
R-4.3-mac-aarch64ERRORMar 29 2025

Exports:calcBatchEffectscalcScorecalcSummaryclearBEgenescorrectBatchEffectcountValuesToPredictfindOutsideValuesimputeMissingDatalocalLosslossmakeBoxplotpreprocessBEclearreplaceOutsideValues

Dependencies:abindaskpassBHBiocParallelcodetoolscpp11data.tabledixonTestformatRfutile.loggerfutile.optionsidslambda.rlatticeMatrixopensslrbibutilsRcppRdpacksnowsysuuid

Detecting and correcting batch effects with BEclear

Livia Rasp, Markus Merl

Rendered fromBEclear.Rmdusingknitr::rmarkdownon Mar 29 2025.

Last update: 2023-04-06
Started: 2018-12-07

Citation

To cite BEclear in publications use:

Akulenko R, Merl M, Helms V (2016). “BEclear: Batch effect detection and adjustment in DNA methylation data.” PLoS ONE, 11(8), 1-17. doi:10.1371/journal.pone.0159921, https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0159921.

Corresponding BibTeX entry: 

  @Article{,
    title = {{BEclear: Batch} effect detection and adjustment in DNA
      methylation data.},
    author = {Ruslan Akulenko and Markus Merl and Volkhard Helms},
    year = {2016},
    url =
      {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0159921},
    doi = {10.1371/journal.pone.0159921},
    journal = {PLoS ONE},
    number = {8},
    pages = {1-17},
    volume = {11},
  }

Readme and manuals

BEclear

Description

This package provides functions to detect and correct for batch effects in DNA methylation data. The core function for the data imputation is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.

Installation

# Installation from Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("BEclear")

# Installation of the development version from GitHub
if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("uds-helms/BEclear", build_opts = c())

Usage example

For example code you can either read the vignette on Bioconductor. Or you can open it local, after you installed the BEclear package with following command:

browseVignettes("BEclear")

Planned features

If you have a suggestion you could either open an issue or write an email under the following address: Livia.Rasp at gmail.com

Citation

Akulenko, R., Merl, M., & Helms, V. (2016). BEclear: Batch effect detection and adjustment in DNA methylation data. PLoS ONE, 11(8), 1–17. https://doi.org/10.1371/journal.pone.0159921

Help Manual

Help pageTopics
Correction of batch effects in DNA methylation dataBEclear-package BEclearCorrected _PACKAGE
Example data set for the BEclear-packageBEclear example methylation data ex.data
Example data set for the BEclear-packageBEclear example sample data ex.samples
Calculate the Batch Effects in a given data setcalcBatchEffects
calculate batch effect scorecalcScore
Summarize median comparison and p-value calculation resultscalcSummary
Prepare a data matrix for the BEclear functionclearBEgenes
Correct a batch effect in DNA methylation datacorrectBatchEffect
Count NA entries in a matrixcountValuesToPredict
Example matrix of corrected data for the BEclear-packageex.corrected.data
Find DNA methylation values out of the boundariesfindOutsideValues
Matrix prediction using a Latent Factor ModelimputeMissingData
lossloss
produce simple predefined boxplot for methylation datamakeBoxplot
preprocessBEclearpreprocessBEclear
Replace DNA methylation values out of the boundariesreplaceOutsideValues