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Batch Effect Removal and Addon Normalization (in Phenotype Prediction using Gene Data)

Installation

About

Various tools dealing with batch effects, in particular enabling the removal of discrepancies between training and test sets in prediction scenarios. Moreover, addon quantile normalization and addon RMA normalization (Kostka & Spang, 2008) is implemented to enable integrating the quantile normalization step into prediction rules. The following batch effect removal methods are implemented: FAbatch, ComBat, (f)SVA, mean-centering, standardization, Ratio-A and Ratio-G. For each of these we provide an additional function which enables a posteriori ('addon') batch effect removal in independent batches ('test data'). Here, the (already batch effect adjusted) training data is not altered. For evaluating the success of batch effect adjustment several metrics are provided. Moreover, the package implements a plot for the visualization of batch effects using principal component analysis. The main functions of the package for batch effect adjustment are ba() and baaddon() which enable batch effect removal and addon batch effect removal, respectively, with one of the seven methods mentioned above. Another important function here is bametric() which is a wrapper function for all implemented methods for evaluating the success of batch effect removal. For (addon) quantile normalization and (addon) RMA normalization the functions qunormtrain(), qunormaddon(), rmatrain() and rmaaddon() can be used.

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Version 1.1
R ≥ 3.1.0
Published 2022-06-22 646 days ago
Needs compilation? no
License GPL-2
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Maintainer

Maintainer

Roman Hornung

hornung@ibe.med.uni-muenchen.de

Authors

Roman Hornung
David Causeur

Material

Reference manual
Package source

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

bapred archive

Depends

R ≥ 3.1.0
glmnet
lme4
MASS
sva
affyPLM

Imports

FNN
fuzzyRankTests
methods
mnormt
affy
Biobase

Suggests

ArrayExpress