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/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)

batcheffect dnamethylation software preprocessing statisticalmethod batch-effects bioconductor-package dna-methylation latent-factor-model methylation missing-data missing-values stochastic-gradient-descent cpp

5.90 score 4 stars 11 scripts 324 downloads 3 mentions 13 exports 22 dependencies

Last updated 2 months agofrom:4a3e2f429e. Checks:OK: 1 NOTE: 7 ERROR: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win-x86_64	NOTE	Nov 29 2024
R-4.5-linux-x86_64	NOTE	Nov 29 2024
R-4.4-win-x86_64	NOTE	Nov 29 2024
R-4.4-mac-x86_64	NOTE	Nov 29 2024
R-4.4-mac-aarch64	NOTE	Nov 29 2024
R-4.3-win-x86_64	NOTE	Nov 29 2024
R-4.3-mac-x86_64	NOTE	Nov 29 2024
R-4.3-mac-aarch64	ERROR	Nov 29 2024

Exports:calcBatchEffects calcScore calcSummary clearBEgenes correctBatchEffect countValuesToPredict findOutsideValues imputeMissingData localLoss loss makeBoxplot preprocessBEclear replaceOutsideValues

Dependencies:abind askpass BH BiocParallel codetools cpp11 data.table dixonTest formatR futile.logger futile.options ids lambda.r lattice Matrix openssl rbibutils Rcpp Rdpack snow sys uuid

Detecting and correcting batch effects with BEclear

Livia Rasp, Markus Merl

Rendered fromBEclear.Rmdusingknitr::rmarkdownon Nov 29 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Correction of batch effects in DNA methylation data	BEclear-package BEclearCorrected _PACKAGE
Example data set for the BEclear-package	BEclear example methylation data ex.data
Example data set for the BEclear-package	BEclear example sample data ex.samples
Calculate the Batch Effects in a given data set	calcBatchEffects
calculate batch effect score	calcScore
Summarize median comparison and p-value calculation results	calcSummary
Prepare a data matrix for the BEclear function	clearBEgenes
Correct a batch effect in DNA methylation data	correctBatchEffect
Count NA entries in a matrix	countValuesToPredict
Example matrix of corrected data for the BEclear-package	ex.corrected.data
Find DNA methylation values out of the boundaries	findOutsideValues
Matrix prediction using a Latent Factor Model	imputeMissingData
loss	loss
produce simple predefined boxplot for methylation data	makeBoxplot
preprocessBEclear	preprocessBEclear
Replace DNA methylation values out of the boundaries	replaceOutsideValues