# Function to normalize the scores per class
# The scores of each class are normalized by dividing the score values for the maximum score of that class
# Input:
# S : matrix with the raw non normalized scores. Rows are examples (proteins), columns are the classes (GO terms)
# Output:
# A score matrix with the same dimensions of S, but with scores max/normalized separately for each class.
normalize.max <- function(S){
	max.class <- apply(S,2,max);
	for(i in 1:ncol(S)){
	 	S[,i] <- S[,i]/max.class[i]
	}
	return(S);
}