R/centerData.R

In pint: Pairwise INTegration of functional genomics data

centerData <- function (X, rm.na = TRUE, meanvalue = NULL) {

  # Shift data matrix (columns) to zero, or given 'meanvalue'
  
  if (!rm.na) {
    xcenter <- colMeans(X)
    X2 <- X - rep(xcenter, rep.int(nrow(X), ncol(X)))
  } else {	
    X2 <- array(NA, dim = c(nrow(X), ncol(X)), dimnames = dimnames(X))
    for (i in 1:ncol(X)) {
      x <- X[,i]
      nainds <- is.na(x)
      xmean <- mean(x[!nainds])
      X2[!nainds,i] <- x[!nainds] - xmean 	
    }
    dimnames(X2) <- dimnames(X)
  }

  if (!is.null(meanvalue)) {
    # Shift the data so that mean gets a specified value
    X2 <- X2 + meanvalue
  }


  
  X2
}