R/sepscore.R

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

Defines functions sepscore

Documented in sepscore

sepscore <-
function(xba, batch, k=10) {

  allpairs <- combn(levels(batch), 2)

  sum(apply(allpairs, 2, function(y) (sum(batch==y[1]) + sum(batch==y[2]))*sepscoreTwo(xba[batch==y[1],], 
    xba[batch==y[2],], k=k))/(nrow(xba)*(length(levels(batch))-1)))

}

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