R/diffexprm.R

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

diffexprm <-
  function(x, batch, y, method=c("fabatch", "combat", "sva", "meancenter", "standardize", "ratioa", "ratiog", "none")) {
    
    if(!(method %in% c("fabatch", "combat", "sva", "meancenter",
                       "standardize", "ratioa", "ratiog", "none")))
      stop("Input parameter 'method' has to be one of the following:\n'fabatch',  'combat', 'fsva', 'meancenter', 'standardize', 'ratioa', 'ratiog', 'none'.")
    
    batchessuited <- apply(table(batch, y), 1, function(x) min(x)>1)
    xbrlist <- lapply(levels(batch)[batchessuited], function(x2)
      ba(x=x[batch!=x2,], y=y[batch!=x2], batch=droplevels(batch[batch!=x2]), method=method)$xadj)
    
    diffexprmAfterBR(x, xbrlist, y, batch, batchessuited)
    
  }