preprocess2.R

# Your new preprocess.R should look like this
input_file <- read.csv(file = 'data/simulation.tsv',
                       sep='\t',
                       stringsAsFactors=FALSE)
input_file <- input_file[, 1:50]
input_file <- lapply(input_file,
                     function(x) replace(x,
                                         is.na(x),
                                         mean(x,
                                              na.rm = TRUE)))
input_file <- as.data.frame(input_file)

input_file[, unlist(lapply(input_file, is.numeric))] <-
  apply(input_file[, unlist(lapply(input_file, is.numeric))],
        2,
        function(x) ifelse(x < 0, -1, x))

input_file[, unlist(lapply(input_file, is.numeric))] <-
  apply(input_file[, unlist(lapply(input_file, is.numeric))],
        2,
        function(x) ifelse(x > 0, 1, x))

write.csv2(input_file,
           'data/simulation_preprocessed.csv',
           row.names=FALSE)