Package: BEclear 2.28.0

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]

BEclear_2.28.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BEclear/json (API)

# Install 'BEclear' in R:

install.packages('BEclear', repos = c('https://bioc-release.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-2.29.1(bioc 3.24)BEclear-2.28.0(bioc 3.23)

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

6.65 score 5 stars 20 scripts 3 mentions 13 exports 23 dependencies

Last updated from:953b198caa (on RELEASE_3_23). Checks:12 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	171
linux-devel-arm64	NOTE	177
linux-devel-x86_64	NOTE	222
source / vignettes	OK	223
linux-release-arm64	NOTE	177
linux-release-x86_64	NOTE	230
macos-release-arm64	NOTE	98
macos-release-x86_64	NOTE	247
macos-oldrel-arm64	NOTE	92
macos-oldrel-x86_64	NOTE	187
windows-devel	NOTE	155
windows-release	NOTE	140
windows-oldrel	NOTE	127
wasm-release	OK	158

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 logger Matrix openssl rbibutils Rcpp Rdpack snow sys uuid

Detecting and correcting batch effects with BEclear

Rendered fromBEclear.Rmdusingknitr::rmarkdown

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 BEclear BEclearCorrected
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