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

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

## Documentation for package ‘bapred’ version 1.1

- DESCRIPTION file.

## Help Pages

bapred-package | The bapred package
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 | 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 (after batch effect adjustment)
fabatch | Batch effect adjustment using FAbatch
fabatchaddon | Addon batch effect adjustment using FAbatch
kldist | Kullback-Leibler divergence between density of within and between batch pairwise distances
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 Analysis
pvcam | Proportion of variation induced by class signal estimated by Principal Variance Component Analysis
qunormaddon | Addon quantile normalization using "documentation by value" (Kostka & Spang, 2008)
qunormtrain | Quantile normalization with "documentation by value" (Kostka & Spang, 2008)
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" (Kostka & Spang, 2008)
rmatrain | RMA normalization with "documentation by value" (Kostka & Spang, 2008)
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'