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

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.

Author
Roman Hornung, David Causeur
Date of publication
2016-06-03 19:12:25
Maintainer
Roman Hornung <hornung@ibe.med.uni-muenchen.de>
License
GPL-2
Version
1.0

View on CRAN

Man pages

autism
Autism dataset
avedist
Average minimal distance between batches
ba
Batch effect adjustment using a method of choice
baaddon
Addon batch effect adjustment
bametric
Diverse metrics for quality of (adjusted) batch data
bapred-internal
Internal bapred functions
bapred-package
The bapred package
batch
batch variable of dataset 'autism'
combatba
Batch effect adjustment using ComBat
combatbaaddon
Addon batch effect adjustment using ComBat
corba
Mean correlation before and after batch effect adjustment
diffexprm
Measure for performance of differential expression analysis...
fabatch
Batch effect adjustment using FAbatch
fabatchaddon
Addon batch effect adjustment using FAbatch
kldist
Kullback-Leibler divergence between density of within and...
meancenter
Batch effect adjustment by mean-centering
meancenteraddon
Addon batch effect adjustment for mean-centering
noba
No batch effect adjustment
nobaaddon
No addon batch effect adjustment
pcplot
Visualization of batch effects using Principal Component...
pvcam
Proportion of variation induced by class signal estimated by...
qunormaddon
Addon quantile normalization using "documentation by value"...
qunormtrain
Quantile normalization with "documentation by value" (Kostka...
ratioa
Batch effect adjustment using Ratio-A
ratioaaddon
Addon batch effect adjustment for Ratio-A
ratiog
Batch effect adjustment using Ratio-G
ratiogaddon
Addon batch effect adjustment for Ratio-G
rmaaddon
Addon RMA normalization using "documentation by value"...
rmatrain
RMA normalization with "documentation by value" (Kostka &...
sepscore
Separation score as described in Hornung et al. (2016)
skewdiv
Skewness divergence score
standardize
Batch effect adjustment by standardization
standardizeaddon
Addon batch effect adjustment for standardization
svaba
Batch effect adjustment using SVA
svabaaddon
Addon batch effect adjustment using frozen SVA
X
Covariate matrix of dataset 'autism'
y
Target variable of dataset 'autism'

Files in this package

bapred
bapred/inst
bapred/inst/CITATION
bapred/NAMESPACE
bapred/data
bapred/data/autism.rda
bapred/R
bapred/R/postvar.R
bapred/R/normalizeqntval.R
bapred/R/normalizeAffyBatchqntval.R
bapred/R/fabatchaddon.R
bapred/R/meancenteraddon.R
bapred/R/rmatrain.R
bapred/R/it.sol.R
bapred/R/mypvcaBatchAssess.R
bapred/R/print.ratioa.R
bapred/R/print.noba.R
bapred/R/svaba.R
bapred/R/combatba.R
bapred/R/qunormaddon.R
bapred/R/ratioaaddon.R
bapred/R/skewdiv.R
bapred/R/aprior.R
bapred/R/VarInflation.R
bapred/R/print.combat.R
bapred/R/bametric.R
bapred/R/plotcomp.R
bapred/R/svabaaddon.R
bapred/R/print.fabatch.R
bapred/R/meancenter.R
bapred/R/normalizeqntadd.R
bapred/R/print.meancenter.R
bapred/R/print.svatrain.R
bapred/R/rmaaddon.R
bapred/R/qunormtrain.R
bapred/R/diffexprmAfterBR.R
bapred/R/design.mat.R
bapred/R/summarizeadd2.R
bapred/R/noba.R
bapred/R/baaddon.R
bapred/R/bprior.R
bapred/R/pcplot.R
bapred/R/pvcam.R
bapred/R/standardize.R
bapred/R/Dt.R
bapred/R/sepscoreTwo.R
bapred/R/postmean.R
bapred/R/build.design.R
bapred/R/skewdivTwo.R
bapred/R/diffexprm.R
bapred/R/print.standardize.R
bapred/R/bivprob.R
bapred/R/emfahighdim.R
bapred/R/kldistTwo.R
bapred/R/ratiogaddon.R
bapred/R/combatbaaddon.R
bapred/R/corba.R
bapred/R/ratiog.R
bapred/R/nobaaddon.R
bapred/R/ratioa.R
bapred/R/kldist.R
bapred/R/print.qunormtrain.R
bapred/R/sepscore.R
bapred/R/avedistTwo.R
bapred/R/nbfactors.R
bapred/R/standardizeaddon.R
bapred/R/ba.R
bapred/R/print.rmatrain.R
bapred/R/extractAffybatch.R
bapred/R/list.batch.R
bapred/R/fuzzywilcox.R
bapred/R/ba-internal.R
bapred/R/avedist.R
bapred/R/print.ratiog.R
bapred/R/normalizeqntadd2.R
bapred/R/summarizeval2.R
bapred/R/fabatch.R
bapred/MD5
bapred/DESCRIPTION
bapred/man
bapred/man/pcplot.Rd
bapred/man/skewdiv.Rd
bapred/man/bapred-package.Rd
bapred/man/diffexprm.Rd
bapred/man/pvcam.Rd
bapred/man/corba.Rd
bapred/man/svaba.Rd
bapred/man/nobaaddon.Rd
bapred/man/standardizeaddon.Rd
bapred/man/y.Rd
bapred/man/batch.Rd
bapred/man/qunormaddon.Rd
bapred/man/ratioa.Rd
bapred/man/rmaaddon.Rd
bapred/man/kldist.Rd
bapred/man/sepscore.Rd
bapred/man/baaddon.Rd
bapred/man/avedist.Rd
bapred/man/ba.Rd
bapred/man/fabatch.Rd
bapred/man/bametric.Rd
bapred/man/combatba.Rd
bapred/man/meancenter.Rd
bapred/man/noba.Rd
bapred/man/bapred-internal.Rd
bapred/man/ratioaaddon.Rd
bapred/man/ratiogaddon.Rd
bapred/man/meancenteraddon.Rd
bapred/man/autism.Rd
bapred/man/combatbaaddon.Rd
bapred/man/X.Rd
bapred/man/rmatrain.Rd
bapred/man/fabatchaddon.Rd
bapred/man/ratiog.Rd
bapred/man/svabaaddon.Rd
bapred/man/qunormtrain.Rd
bapred/man/standardize.Rd