R/vim.singleAdjusted.R

In logicFS: Identification of SNP Interactions

vim.singleAdjusted <- function (primes, mat.eval, cl, 
                                neighbor, set, useN)
{
  # For b-th iteration
  # 1. primes includes all primes P_a^b of the b-th logic regression model
  vec.improve <- numeric(ncol(mat.eval))
  # 2. For each prime P_a found in 1., identify neighbors of P_a, composing primes
  #    of P_a and neighbors of composing primes of P_a. imp.primes includes all 
  #    primes, for wich an improvement is calculated in iteration b
  comp.primes <- unique(getComposingPrimes(primes, colnames(mat.eval)))
  neighborprimes <- unique(unlist(getNeighbor(primes, neighbor, set, 
                                              colnames(mat.eval))))
  neighborcomp.primes <- unique(unlist(getNeighbor(comp.primes, neighbor, 
                                                   set, colnames(mat.eval))))
  imp.primes <- unique(c(primes, neighborprimes, comp.primes, neighborcomp.primes))
  # 3. For each prime i in imp.primes
  for (i in 1:length(imp.primes)){
    tmp.prime <- imp.primes[i]
    # a) Identify neighbors of prime i, extended interactions of prime i 
    #    and extended interactions of neighbor interactions of prime i,
    #    that are part of the logic model.
    neighbortmp.primes <- unique(unlist(getNeighbor(tmp.prime, neighbor, set, primes)))
    ext.tmp.primes <- getExtendedPrimes(tmp.prime, primes)
    ext.neighbortmp.primes <- getExtendedPrimes(neighbortmp.primes, primes)
    setprime <- unique(c(tmp.prime, ext.tmp.primes, neighbortmp.primes, ext.neighbortmp.primes))
    # b) Remove all primes in setprime from the logic model 
    #    and calculate the score of the reduced model.
    red.primes <- primes[!(primes %in% setprime)]
    vec.design <- rowSums(mat.eval[, red.primes, drop = FALSE]) > 0 
    score.red <- sum(vec.design == cl)
    # c) Add prime i to the logic model and calculate the score of the new (full) model
    preds.new <- rowSums(cbind(mat.eval[, tmp.prime, drop = FALSE], vec.design)) > 0 
    score.full <- sum(preds.new == cl)
    # d) Calculate and save improvement
    id.primes <- which(colnames(mat.eval) %in% tmp.prime)
    vec.improve[id.primes] <- score.full - score.red
  }
  if (!useN) 
    vec.improve <- vec.improve/length(cl)
  vec.improve
}