R/preprocess.R

In RAMP: Regularized Generalized Linear Models with Interaction Effects

preprocess <- function(trx, tex, size = ncol(trx)) {
    minx = min(min(trx), min(tex))
    if (minx < 1) {
        trx = trx + 1 - minx
        tex = tex + 1 - minx
    }
    # trx[trx<1] = 1 tex[tex<1] = 1
    
    varx = apply(trx, 2, var)
    ind = sort(varx, index = TRUE, decreasing = TRUE)
    
    trx = trx[, ind$ix[1:size]]
    tex = tex[, ind$ix[1:size]]
    
    trx = log(trx)/log(10)
    tex = log(tex)/log(10)
    trx = scale(trx)
    tex = scale(tex, attr(trx, "scaled:center"), attr(trx, "scaled:scale"))
    
    return(list(trx = trx, tex = tex))
}