Man pages for bapred
Batch Effect Removal and Addon Normalization (in Phenotype Prediction using Gene Data)

autismAutism dataset
avedistAverage minimal distance between batches
baBatch effect adjustment using a method of choice
baaddonAddon batch effect adjustment
bametricDiverse metrics for quality of (adjusted) batch data
bapred-internalInternal bapred functions
bapred-packageThe bapred package
batchbatch variable of dataset 'autism'
combatbaBatch effect adjustment using ComBat
combatbaaddonAddon batch effect adjustment using ComBat
corbaMean correlation before and after batch effect adjustment
diffexprmMeasure for performance of differential expression analysis...
fabatchBatch effect adjustment using FAbatch
fabatchaddonAddon batch effect adjustment using FAbatch
kldistKullback-Leibler divergence between density of within and...
meancenterBatch effect adjustment by mean-centering
meancenteraddonAddon batch effect adjustment for mean-centering
nobaNo batch effect adjustment
nobaaddonNo addon batch effect adjustment
pcplotVisualization of batch effects using Principal Component...
pvcamProportion of variation induced by class signal estimated by...
qunormaddonAddon quantile normalization using "documentation by value"...
qunormtrainQuantile normalization with "documentation by value" (Kostka...
ratioaBatch effect adjustment using Ratio-A
ratioaaddonAddon batch effect adjustment for Ratio-A
ratiogBatch effect adjustment using Ratio-G
ratiogaddonAddon batch effect adjustment for Ratio-G
rmaaddonAddon RMA normalization using "documentation by value"...
rmatrainRMA normalization with "documentation by value" (Kostka &...
sepscoreSeparation score as described in Hornung et al. (2016)
skewdivSkewness divergence score
standardizeBatch effect adjustment by standardization
standardizeaddonAddon batch effect adjustment for standardization
svabaBatch effect adjustment using SVA
svabaaddonAddon batch effect adjustment using frozen SVA
XCovariate matrix of dataset 'autism'
yTarget variable of dataset 'autism'
bapred documentation built on May 1, 2019, 10:54 p.m.