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 |

**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

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

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

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