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


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Documentation for package ‘bapred’ version 1.0

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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'