BEclear: Correct for batch effects in DNA methylation data

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

Author
Markus Merl, Ruslan Akulenko
Date of publication
None
Maintainer
Markus Merl <beclear.package@gmail.com>
License
GPL-2
Version
1.6.0

View on Bioconductor

Man pages

BEclear
Matrix prediction method using a Latent Factor Model
BEclearData
Example data set for the BEclear-package
BEclear-package
Correct for batch effects in DNA methylation data
calcMedians
Calculate median difference values
calcPvalues
Calculate p-values
calcScore
calculate batch effect score
calcSummary
Summarize median comparison and p-value calculation results
clearBEgenes
Prepare a data matrix for the BEclear function
correctBatchEffect
Correct a batch effect in DNA methylation data
countValuesToPredict
Count NA entries in a matrix
ex.corrected.data
Example matrix of corrected data for the BEclear-package
findWrongValues
Find DNA methylation values out of the boundaries
makeBoxplot
produce simple predefined boxplot for methylation data
replaceWrongValues
Replace DNA methylation values out of the boundaries

Files in this package

BEclear/DESCRIPTION
BEclear/NAMESPACE
BEclear/NEWS
BEclear/R
BEclear/R/BEclear.R
BEclear/build
BEclear/build/vignette.rds
BEclear/data
BEclear/data/BEclearCorrected.RData
BEclear/data/BEclearData.RData
BEclear/inst
BEclear/inst/doc
BEclear/inst/doc/BEclear.R
BEclear/inst/doc/BEclear.Rnw
BEclear/inst/doc/BEclear.pdf
BEclear/man
BEclear/man/BEclear-package.Rd
BEclear/man/BEclear.Rd
BEclear/man/BEclearData.Rd
BEclear/man/calcMedians.Rd
BEclear/man/calcPvalues.Rd
BEclear/man/calcScore.Rd
BEclear/man/calcSummary.Rd
BEclear/man/clearBEgenes.Rd
BEclear/man/correctBatchEffect.Rd
BEclear/man/countValuesToPredict.Rd
BEclear/man/ex.corrected.data.Rd
BEclear/man/findWrongValues.Rd
BEclear/man/makeBoxplot.Rd
BEclear/man/replaceWrongValues.Rd
BEclear/vignettes
BEclear/vignettes/BEclear.Rnw