mrmr_kmer_selection.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Loading required package: survival\n",
      "Loading required package: igraph\n",
      "\n",
      "Attaching package: ‘igraph’\n",
      "\n",
      "The following objects are masked from ‘package:stats’:\n",
      "\n",
      "    decompose, spectrum\n",
      "\n",
      "The following object is masked from ‘package:base’:\n",
      "\n",
      "    union\n",
      "\n"
     ]
    }
   ],
   "source": [
    "library(mRMRe)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th scope=col>A</th><th scope=col>C</th><th scope=col>G</th><th scope=col>T</th><th scope=col>Total</th><th scope=col>AA</th><th scope=col>AC</th><th scope=col>AT</th><th scope=col>AG</th><th scope=col>CA</th><th scope=col>⋯</th><th scope=col>GGCT</th><th scope=col>GGCG</th><th scope=col>GGTA</th><th scope=col>GGTC</th><th scope=col>GGTT</th><th scope=col>GGTG</th><th scope=col>GGGA</th><th scope=col>GGGC</th><th scope=col>GGGT</th><th scope=col>GGGG</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><td>0.005439052</td><td>0.004687706</td><td>0.006523157</td><td>0.007229232</td><td>0.006232892</td><td>0.004683231</td><td>0.003610108</td><td>0.005265290</td><td>0.005136523</td><td>0.003745318</td><td>⋯          </td><td>0.03067485 </td><td>0.000000000</td><td>0.000000000</td><td>0.003086420</td><td>0.022321429</td><td>0.003787879</td><td>0.005586592</td><td>0.010416667</td><td>0.026143791</td><td>0.012145749</td></tr>\n",
       "\t<tr><td>0.054571826</td><td>0.058563317</td><td>0.042473001</td><td>0.078470032</td><td>0.065584079</td><td>0.033172889</td><td>0.045820605</td><td>0.058323208</td><td>0.053798324</td><td>0.061246971</td><td>⋯          </td><td>0.04294479 </td><td>0.000000000</td><td>0.041666667</td><td>0.030864198</td><td>0.044642857</td><td>0.030303030</td><td>0.044692737</td><td>0.005208333</td><td>0.019607843</td><td>0.016194332</td></tr>\n",
       "\t<tr><td>0.008037711</td><td>0.002905057</td><td>0.008697543</td><td>0.006703470</td><td>0.006935711</td><td>0.006114219</td><td>0.003887809</td><td>0.006682868</td><td>0.011354420</td><td>0.004846883</td><td>⋯          </td><td>0.01840491 </td><td>0.000000000</td><td>0.011904762</td><td>0.006172840</td><td>0.004464286</td><td>0.007575758</td><td>0.027932961</td><td>0.015625000</td><td>0.026143791</td><td>0.028340081</td></tr>\n",
       "\t<tr><td>0.004774279</td><td>0.004621682</td><td>0.007972748</td><td>0.009003680</td><td>0.006880225</td><td>0.002992065</td><td>0.003054707</td><td>0.004657756</td><td>0.006758583</td><td>0.004406257</td><td>⋯          </td><td>0.01840491 </td><td>0.000000000</td><td>0.005952381</td><td>0.006172840</td><td>0.008928571</td><td>0.026515152</td><td>0.011173184</td><td>0.010416667</td><td>0.006535948</td><td>0.008097166</td></tr>\n",
       "\t<tr><td>0.024234000</td><td>0.018156609</td><td>0.033195622</td><td>0.023002103</td><td>0.027003033</td><td>0.015350592</td><td>0.017772841</td><td>0.015188335</td><td>0.040010814</td><td>0.018726592</td><td>⋯          </td><td>0.01226994 </td><td>0.042105263</td><td>0.053571429</td><td>0.021604938</td><td>0.022321429</td><td>0.064393939</td><td>0.044692737</td><td>0.026041667</td><td>0.058823529</td><td>0.028340081</td></tr>\n",
       "\t<tr><td>0.040369856</td><td>0.035454906</td><td>0.043995071</td><td>0.049158780</td><td>0.046903899</td><td>0.027318850</td><td>0.027770064</td><td>0.033819360</td><td>0.052446607</td><td>0.039215686</td><td>⋯          </td><td>0.12269939 </td><td>0.007894737</td><td>0.023809524</td><td>0.009259259</td><td>0.062500000</td><td>0.041666667</td><td>0.094972067</td><td>0.062500000</td><td>0.071895425</td><td>0.052631579</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|lllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllll}\n",
       " A & C & G & T & Total & AA & AC & AT & AG & CA & ⋯ & GGCT & GGCG & GGTA & GGTC & GGTT & GGTG & GGGA & GGGC & GGGT & GGGG\\\\\n",
       "\\hline\n",
       "\t 0.005439052 & 0.004687706 & 0.006523157 & 0.007229232 & 0.006232892 & 0.004683231 & 0.003610108 & 0.005265290 & 0.005136523 & 0.003745318 & ⋯           & 0.03067485  & 0.000000000 & 0.000000000 & 0.003086420 & 0.022321429 & 0.003787879 & 0.005586592 & 0.010416667 & 0.026143791 & 0.012145749\\\\\n",
       "\t 0.054571826 & 0.058563317 & 0.042473001 & 0.078470032 & 0.065584079 & 0.033172889 & 0.045820605 & 0.058323208 & 0.053798324 & 0.061246971 & ⋯           & 0.04294479  & 0.000000000 & 0.041666667 & 0.030864198 & 0.044642857 & 0.030303030 & 0.044692737 & 0.005208333 & 0.019607843 & 0.016194332\\\\\n",
       "\t 0.008037711 & 0.002905057 & 0.008697543 & 0.006703470 & 0.006935711 & 0.006114219 & 0.003887809 & 0.006682868 & 0.011354420 & 0.004846883 & ⋯           & 0.01840491  & 0.000000000 & 0.011904762 & 0.006172840 & 0.004464286 & 0.007575758 & 0.027932961 & 0.015625000 & 0.026143791 & 0.028340081\\\\\n",
       "\t 0.004774279 & 0.004621682 & 0.007972748 & 0.009003680 & 0.006880225 & 0.002992065 & 0.003054707 & 0.004657756 & 0.006758583 & 0.004406257 & ⋯           & 0.01840491  & 0.000000000 & 0.005952381 & 0.006172840 & 0.008928571 & 0.026515152 & 0.011173184 & 0.010416667 & 0.006535948 & 0.008097166\\\\\n",
       "\t 0.024234000 & 0.018156609 & 0.033195622 & 0.023002103 & 0.027003033 & 0.015350592 & 0.017772841 & 0.015188335 & 0.040010814 & 0.018726592 & ⋯           & 0.01226994  & 0.042105263 & 0.053571429 & 0.021604938 & 0.022321429 & 0.064393939 & 0.044692737 & 0.026041667 & 0.058823529 & 0.028340081\\\\\n",
       "\t 0.040369856 & 0.035454906 & 0.043995071 & 0.049158780 & 0.046903899 & 0.027318850 & 0.027770064 & 0.033819360 & 0.052446607 & 0.039215686 & ⋯           & 0.12269939  & 0.007894737 & 0.023809524 & 0.009259259 & 0.062500000 & 0.041666667 & 0.094972067 & 0.062500000 & 0.071895425 & 0.052631579\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A | C | G | T | Total | AA | AC | AT | AG | CA | ⋯ | GGCT | GGCG | GGTA | GGTC | GGTT | GGTG | GGGA | GGGC | GGGT | GGGG | \n",
       "|---|---|---|---|---|---|\n",
       "| 0.005439052 | 0.004687706 | 0.006523157 | 0.007229232 | 0.006232892 | 0.004683231 | 0.003610108 | 0.005265290 | 0.005136523 | 0.003745318 | ⋯           | 0.03067485  | 0.000000000 | 0.000000000 | 0.003086420 | 0.022321429 | 0.003787879 | 0.005586592 | 0.010416667 | 0.026143791 | 0.012145749 | \n",
       "| 0.054571826 | 0.058563317 | 0.042473001 | 0.078470032 | 0.065584079 | 0.033172889 | 0.045820605 | 0.058323208 | 0.053798324 | 0.061246971 | ⋯           | 0.04294479  | 0.000000000 | 0.041666667 | 0.030864198 | 0.044642857 | 0.030303030 | 0.044692737 | 0.005208333 | 0.019607843 | 0.016194332 | \n",
       "| 0.008037711 | 0.002905057 | 0.008697543 | 0.006703470 | 0.006935711 | 0.006114219 | 0.003887809 | 0.006682868 | 0.011354420 | 0.004846883 | ⋯           | 0.01840491  | 0.000000000 | 0.011904762 | 0.006172840 | 0.004464286 | 0.007575758 | 0.027932961 | 0.015625000 | 0.026143791 | 0.028340081 | \n",
       "| 0.004774279 | 0.004621682 | 0.007972748 | 0.009003680 | 0.006880225 | 0.002992065 | 0.003054707 | 0.004657756 | 0.006758583 | 0.004406257 | ⋯           | 0.01840491  | 0.000000000 | 0.005952381 | 0.006172840 | 0.008928571 | 0.026515152 | 0.011173184 | 0.010416667 | 0.006535948 | 0.008097166 | \n",
       "| 0.024234000 | 0.018156609 | 0.033195622 | 0.023002103 | 0.027003033 | 0.015350592 | 0.017772841 | 0.015188335 | 0.040010814 | 0.018726592 | ⋯           | 0.01226994  | 0.042105263 | 0.053571429 | 0.021604938 | 0.022321429 | 0.064393939 | 0.044692737 | 0.026041667 | 0.058823529 | 0.028340081 | \n",
       "| 0.040369856 | 0.035454906 | 0.043995071 | 0.049158780 | 0.046903899 | 0.027318850 | 0.027770064 | 0.033819360 | 0.052446607 | 0.039215686 | ⋯           | 0.12269939  | 0.007894737 | 0.023809524 | 0.009259259 | 0.062500000 | 0.041666667 | 0.094972067 | 0.062500000 | 0.071895425 | 0.052631579 | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "  A           C           G           T           Total       AA         \n",
       "1 0.005439052 0.004687706 0.006523157 0.007229232 0.006232892 0.004683231\n",
       "2 0.054571826 0.058563317 0.042473001 0.078470032 0.065584079 0.033172889\n",
       "3 0.008037711 0.002905057 0.008697543 0.006703470 0.006935711 0.006114219\n",
       "4 0.004774279 0.004621682 0.007972748 0.009003680 0.006880225 0.002992065\n",
       "5 0.024234000 0.018156609 0.033195622 0.023002103 0.027003033 0.015350592\n",
       "6 0.040369856 0.035454906 0.043995071 0.049158780 0.046903899 0.027318850\n",
       "  AC          AT          AG          CA          ⋯ GGCT       GGCG       \n",
       "1 0.003610108 0.005265290 0.005136523 0.003745318 ⋯ 0.03067485 0.000000000\n",
       "2 0.045820605 0.058323208 0.053798324 0.061246971 ⋯ 0.04294479 0.000000000\n",
       "3 0.003887809 0.006682868 0.011354420 0.004846883 ⋯ 0.01840491 0.000000000\n",
       "4 0.003054707 0.004657756 0.006758583 0.004406257 ⋯ 0.01840491 0.000000000\n",
       "5 0.017772841 0.015188335 0.040010814 0.018726592 ⋯ 0.01226994 0.042105263\n",
       "6 0.027770064 0.033819360 0.052446607 0.039215686 ⋯ 0.12269939 0.007894737\n",
       "  GGTA        GGTC        GGTT        GGTG        GGGA        GGGC       \n",
       "1 0.000000000 0.003086420 0.022321429 0.003787879 0.005586592 0.010416667\n",
       "2 0.041666667 0.030864198 0.044642857 0.030303030 0.044692737 0.005208333\n",
       "3 0.011904762 0.006172840 0.004464286 0.007575758 0.027932961 0.015625000\n",
       "4 0.005952381 0.006172840 0.008928571 0.026515152 0.011173184 0.010416667\n",
       "5 0.053571429 0.021604938 0.022321429 0.064393939 0.044692737 0.026041667\n",
       "6 0.023809524 0.009259259 0.062500000 0.041666667 0.094972067 0.062500000\n",
       "  GGGT        GGGG       \n",
       "1 0.026143791 0.012145749\n",
       "2 0.019607843 0.016194332\n",
       "3 0.026143791 0.028340081\n",
       "4 0.006535948 0.008097166\n",
       "5 0.058823529 0.028340081\n",
       "6 0.071895425 0.052631579"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th scope=col>class_lev1</th><th scope=col>class_lev2</th><th scope=col>class_lev3</th><th scope=col>class_lev4</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><td>1 </td><td>4 </td><td>NA</td><td>NA</td></tr>\n",
       "\t<tr><td>1 </td><td>4 </td><td>NA</td><td>NA</td></tr>\n",
       "\t<tr><td>1 </td><td>4 </td><td>NA</td><td>NA</td></tr>\n",
       "\t<tr><td>1 </td><td>4 </td><td>NA</td><td>NA</td></tr>\n",
       "\t<tr><td>1 </td><td>4 </td><td>NA</td><td>NA</td></tr>\n",
       "\t<tr><td>1 </td><td>4 </td><td>NA</td><td>NA</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|llll}\n",
       " class\\_lev1 & class\\_lev2 & class\\_lev3 & class\\_lev4\\\\\n",
       "\\hline\n",
       "\t 1  & 4  & NA & NA\\\\\n",
       "\t 1  & 4  & NA & NA\\\\\n",
       "\t 1  & 4  & NA & NA\\\\\n",
       "\t 1  & 4  & NA & NA\\\\\n",
       "\t 1  & 4  & NA & NA\\\\\n",
       "\t 1  & 4  & NA & NA\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "class_lev1 | class_lev2 | class_lev3 | class_lev4 | \n",
       "|---|---|---|---|---|---|\n",
       "| 1  | 4  | NA | NA | \n",
       "| 1  | 4  | NA | NA | \n",
       "| 1  | 4  | NA | NA | \n",
       "| 1  | 4  | NA | NA | \n",
       "| 1  | 4  | NA | NA | \n",
       "| 1  | 4  | NA | NA | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "  class_lev1 class_lev2 class_lev3 class_lev4\n",
       "1 1          4          NA         NA        \n",
       "2 1          4          NA         NA        \n",
       "3 1          4          NA         NA        \n",
       "4 1          4          NA         NA        \n",
       "5 1          4          NA         NA        \n",
       "6 1          4          NA         NA        "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "data <- read.csv('./raw_data')\n",
    "data[1:length(data[1,])] <- lapply(data[1:length(data[1,])], as.numeric)\n",
    "target <- data[,(length(data[1,])-3):(length(data[1,]))]\n",
    "data <- data[,1:(length(data[1,])-4)]\n",
    "data <- apply(data, 2, function(x)(x-min(x))/(max(x)-min(x))); data <- data.frame(data) # Normalize features from 0 to 1\n",
    "head(data)\n",
    "head(target)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th scope=col>target</th><th scope=col>A</th><th scope=col>C</th><th scope=col>G</th><th scope=col>T</th><th scope=col>Total</th><th scope=col>AA</th><th scope=col>AC</th><th scope=col>AT</th><th scope=col>AG</th><th scope=col>⋯</th><th scope=col>GGCT</th><th scope=col>GGCG</th><th scope=col>GGTA</th><th scope=col>GGTC</th><th scope=col>GGTT</th><th scope=col>GGTG</th><th scope=col>GGGA</th><th scope=col>GGGC</th><th scope=col>GGGT</th><th scope=col>GGGG</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><td>1          </td><td>0.005439052</td><td>0.004687706</td><td>0.006523157</td><td>0.007229232</td><td>0.006232892</td><td>0.004683231</td><td>0.003610108</td><td>0.005265290</td><td>0.005136523</td><td>⋯          </td><td>0.03067485 </td><td>0.000000000</td><td>0.000000000</td><td>0.003086420</td><td>0.022321429</td><td>0.003787879</td><td>0.005586592</td><td>0.010416667</td><td>0.026143791</td><td>0.012145749</td></tr>\n",
       "\t<tr><td>1          </td><td>0.054571826</td><td>0.058563317</td><td>0.042473001</td><td>0.078470032</td><td>0.065584079</td><td>0.033172889</td><td>0.045820605</td><td>0.058323208</td><td>0.053798324</td><td>⋯          </td><td>0.04294479 </td><td>0.000000000</td><td>0.041666667</td><td>0.030864198</td><td>0.044642857</td><td>0.030303030</td><td>0.044692737</td><td>0.005208333</td><td>0.019607843</td><td>0.016194332</td></tr>\n",
       "\t<tr><td>1          </td><td>0.008037711</td><td>0.002905057</td><td>0.008697543</td><td>0.006703470</td><td>0.006935711</td><td>0.006114219</td><td>0.003887809</td><td>0.006682868</td><td>0.011354420</td><td>⋯          </td><td>0.01840491 </td><td>0.000000000</td><td>0.011904762</td><td>0.006172840</td><td>0.004464286</td><td>0.007575758</td><td>0.027932961</td><td>0.015625000</td><td>0.026143791</td><td>0.028340081</td></tr>\n",
       "\t<tr><td>1          </td><td>0.004774279</td><td>0.004621682</td><td>0.007972748</td><td>0.009003680</td><td>0.006880225</td><td>0.002992065</td><td>0.003054707</td><td>0.004657756</td><td>0.006758583</td><td>⋯          </td><td>0.01840491 </td><td>0.000000000</td><td>0.005952381</td><td>0.006172840</td><td>0.008928571</td><td>0.026515152</td><td>0.011173184</td><td>0.010416667</td><td>0.006535948</td><td>0.008097166</td></tr>\n",
       "\t<tr><td>1          </td><td>0.024234000</td><td>0.018156609</td><td>0.033195622</td><td>0.023002103</td><td>0.027003033</td><td>0.015350592</td><td>0.017772841</td><td>0.015188335</td><td>0.040010814</td><td>⋯          </td><td>0.01226994 </td><td>0.042105263</td><td>0.053571429</td><td>0.021604938</td><td>0.022321429</td><td>0.064393939</td><td>0.044692737</td><td>0.026041667</td><td>0.058823529</td><td>0.028340081</td></tr>\n",
       "\t<tr><td>1          </td><td>0.040369856</td><td>0.035454906</td><td>0.043995071</td><td>0.049158780</td><td>0.046903899</td><td>0.027318850</td><td>0.027770064</td><td>0.033819360</td><td>0.052446607</td><td>⋯          </td><td>0.12269939 </td><td>0.007894737</td><td>0.023809524</td><td>0.009259259</td><td>0.062500000</td><td>0.041666667</td><td>0.094972067</td><td>0.062500000</td><td>0.071895425</td><td>0.052631579</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|llllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllll}\n",
       " target & A & C & G & T & Total & AA & AC & AT & AG & ⋯ & GGCT & GGCG & GGTA & GGTC & GGTT & GGTG & GGGA & GGGC & GGGT & GGGG\\\\\n",
       "\\hline\n",
       "\t 1           & 0.005439052 & 0.004687706 & 0.006523157 & 0.007229232 & 0.006232892 & 0.004683231 & 0.003610108 & 0.005265290 & 0.005136523 & ⋯           & 0.03067485  & 0.000000000 & 0.000000000 & 0.003086420 & 0.022321429 & 0.003787879 & 0.005586592 & 0.010416667 & 0.026143791 & 0.012145749\\\\\n",
       "\t 1           & 0.054571826 & 0.058563317 & 0.042473001 & 0.078470032 & 0.065584079 & 0.033172889 & 0.045820605 & 0.058323208 & 0.053798324 & ⋯           & 0.04294479  & 0.000000000 & 0.041666667 & 0.030864198 & 0.044642857 & 0.030303030 & 0.044692737 & 0.005208333 & 0.019607843 & 0.016194332\\\\\n",
       "\t 1           & 0.008037711 & 0.002905057 & 0.008697543 & 0.006703470 & 0.006935711 & 0.006114219 & 0.003887809 & 0.006682868 & 0.011354420 & ⋯           & 0.01840491  & 0.000000000 & 0.011904762 & 0.006172840 & 0.004464286 & 0.007575758 & 0.027932961 & 0.015625000 & 0.026143791 & 0.028340081\\\\\n",
       "\t 1           & 0.004774279 & 0.004621682 & 0.007972748 & 0.009003680 & 0.006880225 & 0.002992065 & 0.003054707 & 0.004657756 & 0.006758583 & ⋯           & 0.01840491  & 0.000000000 & 0.005952381 & 0.006172840 & 0.008928571 & 0.026515152 & 0.011173184 & 0.010416667 & 0.006535948 & 0.008097166\\\\\n",
       "\t 1           & 0.024234000 & 0.018156609 & 0.033195622 & 0.023002103 & 0.027003033 & 0.015350592 & 0.017772841 & 0.015188335 & 0.040010814 & ⋯           & 0.01226994  & 0.042105263 & 0.053571429 & 0.021604938 & 0.022321429 & 0.064393939 & 0.044692737 & 0.026041667 & 0.058823529 & 0.028340081\\\\\n",
       "\t 1           & 0.040369856 & 0.035454906 & 0.043995071 & 0.049158780 & 0.046903899 & 0.027318850 & 0.027770064 & 0.033819360 & 0.052446607 & ⋯           & 0.12269939  & 0.007894737 & 0.023809524 & 0.009259259 & 0.062500000 & 0.041666667 & 0.094972067 & 0.062500000 & 0.071895425 & 0.052631579\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "target | A | C | G | T | Total | AA | AC | AT | AG | ⋯ | GGCT | GGCG | GGTA | GGTC | GGTT | GGTG | GGGA | GGGC | GGGT | GGGG | \n",
       "|---|---|---|---|---|---|\n",
       "| 1           | 0.005439052 | 0.004687706 | 0.006523157 | 0.007229232 | 0.006232892 | 0.004683231 | 0.003610108 | 0.005265290 | 0.005136523 | ⋯           | 0.03067485  | 0.000000000 | 0.000000000 | 0.003086420 | 0.022321429 | 0.003787879 | 0.005586592 | 0.010416667 | 0.026143791 | 0.012145749 | \n",
       "| 1           | 0.054571826 | 0.058563317 | 0.042473001 | 0.078470032 | 0.065584079 | 0.033172889 | 0.045820605 | 0.058323208 | 0.053798324 | ⋯           | 0.04294479  | 0.000000000 | 0.041666667 | 0.030864198 | 0.044642857 | 0.030303030 | 0.044692737 | 0.005208333 | 0.019607843 | 0.016194332 | \n",
       "| 1           | 0.008037711 | 0.002905057 | 0.008697543 | 0.006703470 | 0.006935711 | 0.006114219 | 0.003887809 | 0.006682868 | 0.011354420 | ⋯           | 0.01840491  | 0.000000000 | 0.011904762 | 0.006172840 | 0.004464286 | 0.007575758 | 0.027932961 | 0.015625000 | 0.026143791 | 0.028340081 | \n",
       "| 1           | 0.004774279 | 0.004621682 | 0.007972748 | 0.009003680 | 0.006880225 | 0.002992065 | 0.003054707 | 0.004657756 | 0.006758583 | ⋯           | 0.01840491  | 0.000000000 | 0.005952381 | 0.006172840 | 0.008928571 | 0.026515152 | 0.011173184 | 0.010416667 | 0.006535948 | 0.008097166 | \n",
       "| 1           | 0.024234000 | 0.018156609 | 0.033195622 | 0.023002103 | 0.027003033 | 0.015350592 | 0.017772841 | 0.015188335 | 0.040010814 | ⋯           | 0.01226994  | 0.042105263 | 0.053571429 | 0.021604938 | 0.022321429 | 0.064393939 | 0.044692737 | 0.026041667 | 0.058823529 | 0.028340081 | \n",
       "| 1           | 0.040369856 | 0.035454906 | 0.043995071 | 0.049158780 | 0.046903899 | 0.027318850 | 0.027770064 | 0.033819360 | 0.052446607 | ⋯           | 0.12269939  | 0.007894737 | 0.023809524 | 0.009259259 | 0.062500000 | 0.041666667 | 0.094972067 | 0.062500000 | 0.071895425 | 0.052631579 | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "  target A           C           G           T           Total      \n",
       "1 1      0.005439052 0.004687706 0.006523157 0.007229232 0.006232892\n",
       "2 1      0.054571826 0.058563317 0.042473001 0.078470032 0.065584079\n",
       "3 1      0.008037711 0.002905057 0.008697543 0.006703470 0.006935711\n",
       "4 1      0.004774279 0.004621682 0.007972748 0.009003680 0.006880225\n",
       "5 1      0.024234000 0.018156609 0.033195622 0.023002103 0.027003033\n",
       "6 1      0.040369856 0.035454906 0.043995071 0.049158780 0.046903899\n",
       "  AA          AC          AT          AG          ⋯ GGCT       GGCG       \n",
       "1 0.004683231 0.003610108 0.005265290 0.005136523 ⋯ 0.03067485 0.000000000\n",
       "2 0.033172889 0.045820605 0.058323208 0.053798324 ⋯ 0.04294479 0.000000000\n",
       "3 0.006114219 0.003887809 0.006682868 0.011354420 ⋯ 0.01840491 0.000000000\n",
       "4 0.002992065 0.003054707 0.004657756 0.006758583 ⋯ 0.01840491 0.000000000\n",
       "5 0.015350592 0.017772841 0.015188335 0.040010814 ⋯ 0.01226994 0.042105263\n",
       "6 0.027318850 0.027770064 0.033819360 0.052446607 ⋯ 0.12269939 0.007894737\n",
       "  GGTA        GGTC        GGTT        GGTG        GGGA        GGGC       \n",
       "1 0.000000000 0.003086420 0.022321429 0.003787879 0.005586592 0.010416667\n",
       "2 0.041666667 0.030864198 0.044642857 0.030303030 0.044692737 0.005208333\n",
       "3 0.011904762 0.006172840 0.004464286 0.007575758 0.027932961 0.015625000\n",
       "4 0.005952381 0.006172840 0.008928571 0.026515152 0.011173184 0.010416667\n",
       "5 0.053571429 0.021604938 0.022321429 0.064393939 0.044692737 0.026041667\n",
       "6 0.023809524 0.009259259 0.062500000 0.041666667 0.094972067 0.062500000\n",
       "  GGGT        GGGG       \n",
       "1 0.026143791 0.012145749\n",
       "2 0.019607843 0.016194332\n",
       "3 0.026143791 0.028340081\n",
       "4 0.006535948 0.008097166\n",
       "5 0.058823529 0.028340081\n",
       "6 0.071895425 0.052631579"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Root node features\n",
    "indx <- !is.na(target[,1]) # Those with known class\n",
    "tmp <- cbind(target[indx,1],data[indx,])\n",
    "names(tmp)[1] <- 'target'\n",
    "head(tmp)\n",
    "# res_root <- mRMR.ensemble(data = mRMR.data(tmp), solution_count=5, target_indices = 1, feature_count = 300, method='bootstrap')\n",
    "res_root <- mRMR.ensemble(data = mRMR.data(tmp), solution_count=1, target_indices = 1, feature_count = 300, method='exhaustive')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th scope=col>target</th><th scope=col>A</th><th scope=col>C</th><th scope=col>G</th><th scope=col>T</th><th scope=col>Total</th><th scope=col>AA</th><th scope=col>AC</th><th scope=col>AT</th><th scope=col>AG</th><th scope=col>⋯</th><th scope=col>GGCT</th><th scope=col>GGCG</th><th scope=col>GGTA</th><th scope=col>GGTC</th><th scope=col>GGTT</th><th scope=col>GGTG</th><th scope=col>GGGA</th><th scope=col>GGGC</th><th scope=col>GGGT</th><th scope=col>GGGG</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><td>4          </td><td>0.005439052</td><td>0.004687706</td><td>0.006523157</td><td>0.007229232</td><td>0.006232892</td><td>0.004683231</td><td>0.003610108</td><td>0.005265290</td><td>0.005136523</td><td>⋯          </td><td>0.03067485 </td><td>0.000000000</td><td>0.000000000</td><td>0.003086420</td><td>0.022321429</td><td>0.003787879</td><td>0.005586592</td><td>0.010416667</td><td>0.026143791</td><td>0.012145749</td></tr>\n",
       "\t<tr><td>4          </td><td>0.054571826</td><td>0.058563317</td><td>0.042473001</td><td>0.078470032</td><td>0.065584079</td><td>0.033172889</td><td>0.045820605</td><td>0.058323208</td><td>0.053798324</td><td>⋯          </td><td>0.04294479 </td><td>0.000000000</td><td>0.041666667</td><td>0.030864198</td><td>0.044642857</td><td>0.030303030</td><td>0.044692737</td><td>0.005208333</td><td>0.019607843</td><td>0.016194332</td></tr>\n",
       "\t<tr><td>4          </td><td>0.008037711</td><td>0.002905057</td><td>0.008697543</td><td>0.006703470</td><td>0.006935711</td><td>0.006114219</td><td>0.003887809</td><td>0.006682868</td><td>0.011354420</td><td>⋯          </td><td>0.01840491 </td><td>0.000000000</td><td>0.011904762</td><td>0.006172840</td><td>0.004464286</td><td>0.007575758</td><td>0.027932961</td><td>0.015625000</td><td>0.026143791</td><td>0.028340081</td></tr>\n",
       "\t<tr><td>4          </td><td>0.004774279</td><td>0.004621682</td><td>0.007972748</td><td>0.009003680</td><td>0.006880225</td><td>0.002992065</td><td>0.003054707</td><td>0.004657756</td><td>0.006758583</td><td>⋯          </td><td>0.01840491 </td><td>0.000000000</td><td>0.005952381</td><td>0.006172840</td><td>0.008928571</td><td>0.026515152</td><td>0.011173184</td><td>0.010416667</td><td>0.006535948</td><td>0.008097166</td></tr>\n",
       "\t<tr><td>4          </td><td>0.024234000</td><td>0.018156609</td><td>0.033195622</td><td>0.023002103</td><td>0.027003033</td><td>0.015350592</td><td>0.017772841</td><td>0.015188335</td><td>0.040010814</td><td>⋯          </td><td>0.01226994 </td><td>0.042105263</td><td>0.053571429</td><td>0.021604938</td><td>0.022321429</td><td>0.064393939</td><td>0.044692737</td><td>0.026041667</td><td>0.058823529</td><td>0.028340081</td></tr>\n",
       "\t<tr><td>4          </td><td>0.040369856</td><td>0.035454906</td><td>0.043995071</td><td>0.049158780</td><td>0.046903899</td><td>0.027318850</td><td>0.027770064</td><td>0.033819360</td><td>0.052446607</td><td>⋯          </td><td>0.12269939 </td><td>0.007894737</td><td>0.023809524</td><td>0.009259259</td><td>0.062500000</td><td>0.041666667</td><td>0.094972067</td><td>0.062500000</td><td>0.071895425</td><td>0.052631579</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|llllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllll}\n",
       " target & A & C & G & T & Total & AA & AC & AT & AG & ⋯ & GGCT & GGCG & GGTA & GGTC & GGTT & GGTG & GGGA & GGGC & GGGT & GGGG\\\\\n",
       "\\hline\n",
       "\t 4           & 0.005439052 & 0.004687706 & 0.006523157 & 0.007229232 & 0.006232892 & 0.004683231 & 0.003610108 & 0.005265290 & 0.005136523 & ⋯           & 0.03067485  & 0.000000000 & 0.000000000 & 0.003086420 & 0.022321429 & 0.003787879 & 0.005586592 & 0.010416667 & 0.026143791 & 0.012145749\\\\\n",
       "\t 4           & 0.054571826 & 0.058563317 & 0.042473001 & 0.078470032 & 0.065584079 & 0.033172889 & 0.045820605 & 0.058323208 & 0.053798324 & ⋯           & 0.04294479  & 0.000000000 & 0.041666667 & 0.030864198 & 0.044642857 & 0.030303030 & 0.044692737 & 0.005208333 & 0.019607843 & 0.016194332\\\\\n",
       "\t 4           & 0.008037711 & 0.002905057 & 0.008697543 & 0.006703470 & 0.006935711 & 0.006114219 & 0.003887809 & 0.006682868 & 0.011354420 & ⋯           & 0.01840491  & 0.000000000 & 0.011904762 & 0.006172840 & 0.004464286 & 0.007575758 & 0.027932961 & 0.015625000 & 0.026143791 & 0.028340081\\\\\n",
       "\t 4           & 0.004774279 & 0.004621682 & 0.007972748 & 0.009003680 & 0.006880225 & 0.002992065 & 0.003054707 & 0.004657756 & 0.006758583 & ⋯           & 0.01840491  & 0.000000000 & 0.005952381 & 0.006172840 & 0.008928571 & 0.026515152 & 0.011173184 & 0.010416667 & 0.006535948 & 0.008097166\\\\\n",
       "\t 4           & 0.024234000 & 0.018156609 & 0.033195622 & 0.023002103 & 0.027003033 & 0.015350592 & 0.017772841 & 0.015188335 & 0.040010814 & ⋯           & 0.01226994  & 0.042105263 & 0.053571429 & 0.021604938 & 0.022321429 & 0.064393939 & 0.044692737 & 0.026041667 & 0.058823529 & 0.028340081\\\\\n",
       "\t 4           & 0.040369856 & 0.035454906 & 0.043995071 & 0.049158780 & 0.046903899 & 0.027318850 & 0.027770064 & 0.033819360 & 0.052446607 & ⋯           & 0.12269939  & 0.007894737 & 0.023809524 & 0.009259259 & 0.062500000 & 0.041666667 & 0.094972067 & 0.062500000 & 0.071895425 & 0.052631579\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "target | A | C | G | T | Total | AA | AC | AT | AG | ⋯ | GGCT | GGCG | GGTA | GGTC | GGTT | GGTG | GGGA | GGGC | GGGT | GGGG | \n",
       "|---|---|---|---|---|---|\n",
       "| 4           | 0.005439052 | 0.004687706 | 0.006523157 | 0.007229232 | 0.006232892 | 0.004683231 | 0.003610108 | 0.005265290 | 0.005136523 | ⋯           | 0.03067485  | 0.000000000 | 0.000000000 | 0.003086420 | 0.022321429 | 0.003787879 | 0.005586592 | 0.010416667 | 0.026143791 | 0.012145749 | \n",
       "| 4           | 0.054571826 | 0.058563317 | 0.042473001 | 0.078470032 | 0.065584079 | 0.033172889 | 0.045820605 | 0.058323208 | 0.053798324 | ⋯           | 0.04294479  | 0.000000000 | 0.041666667 | 0.030864198 | 0.044642857 | 0.030303030 | 0.044692737 | 0.005208333 | 0.019607843 | 0.016194332 | \n",
       "| 4           | 0.008037711 | 0.002905057 | 0.008697543 | 0.006703470 | 0.006935711 | 0.006114219 | 0.003887809 | 0.006682868 | 0.011354420 | ⋯           | 0.01840491  | 0.000000000 | 0.011904762 | 0.006172840 | 0.004464286 | 0.007575758 | 0.027932961 | 0.015625000 | 0.026143791 | 0.028340081 | \n",
       "| 4           | 0.004774279 | 0.004621682 | 0.007972748 | 0.009003680 | 0.006880225 | 0.002992065 | 0.003054707 | 0.004657756 | 0.006758583 | ⋯           | 0.01840491  | 0.000000000 | 0.005952381 | 0.006172840 | 0.008928571 | 0.026515152 | 0.011173184 | 0.010416667 | 0.006535948 | 0.008097166 | \n",
       "| 4           | 0.024234000 | 0.018156609 | 0.033195622 | 0.023002103 | 0.027003033 | 0.015350592 | 0.017772841 | 0.015188335 | 0.040010814 | ⋯           | 0.01226994  | 0.042105263 | 0.053571429 | 0.021604938 | 0.022321429 | 0.064393939 | 0.044692737 | 0.026041667 | 0.058823529 | 0.028340081 | \n",
       "| 4           | 0.040369856 | 0.035454906 | 0.043995071 | 0.049158780 | 0.046903899 | 0.027318850 | 0.027770064 | 0.033819360 | 0.052446607 | ⋯           | 0.12269939  | 0.007894737 | 0.023809524 | 0.009259259 | 0.062500000 | 0.041666667 | 0.094972067 | 0.062500000 | 0.071895425 | 0.052631579 | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "  target A           C           G           T           Total      \n",
       "1 4      0.005439052 0.004687706 0.006523157 0.007229232 0.006232892\n",
       "2 4      0.054571826 0.058563317 0.042473001 0.078470032 0.065584079\n",
       "3 4      0.008037711 0.002905057 0.008697543 0.006703470 0.006935711\n",
       "4 4      0.004774279 0.004621682 0.007972748 0.009003680 0.006880225\n",
       "5 4      0.024234000 0.018156609 0.033195622 0.023002103 0.027003033\n",
       "6 4      0.040369856 0.035454906 0.043995071 0.049158780 0.046903899\n",
       "  AA          AC          AT          AG          ⋯ GGCT       GGCG       \n",
       "1 0.004683231 0.003610108 0.005265290 0.005136523 ⋯ 0.03067485 0.000000000\n",
       "2 0.033172889 0.045820605 0.058323208 0.053798324 ⋯ 0.04294479 0.000000000\n",
       "3 0.006114219 0.003887809 0.006682868 0.011354420 ⋯ 0.01840491 0.000000000\n",
       "4 0.002992065 0.003054707 0.004657756 0.006758583 ⋯ 0.01840491 0.000000000\n",
       "5 0.015350592 0.017772841 0.015188335 0.040010814 ⋯ 0.01226994 0.042105263\n",
       "6 0.027318850 0.027770064 0.033819360 0.052446607 ⋯ 0.12269939 0.007894737\n",
       "  GGTA        GGTC        GGTT        GGTG        GGGA        GGGC       \n",
       "1 0.000000000 0.003086420 0.022321429 0.003787879 0.005586592 0.010416667\n",
       "2 0.041666667 0.030864198 0.044642857 0.030303030 0.044692737 0.005208333\n",
       "3 0.011904762 0.006172840 0.004464286 0.007575758 0.027932961 0.015625000\n",
       "4 0.005952381 0.006172840 0.008928571 0.026515152 0.011173184 0.010416667\n",
       "5 0.053571429 0.021604938 0.022321429 0.064393939 0.044692737 0.026041667\n",
       "6 0.023809524 0.009259259 0.062500000 0.041666667 0.094972067 0.062500000\n",
       "  GGGT        GGGG       \n",
       "1 0.026143791 0.012145749\n",
       "2 0.019607843 0.016194332\n",
       "3 0.026143791 0.028340081\n",
       "4 0.006535948 0.008097166\n",
       "5 0.058823529 0.028340081\n",
       "6 0.071895425 0.052631579"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Class 1 node features\n",
    "indx <- target[,1]==1 & !is.na(target[,2]) # Those in class 1 with known order\n",
    "tmp <- cbind(target[indx,2],data[indx,])\n",
    "names(tmp)[1] <- 'target'\n",
    "head(tmp)\n",
    "# res_class1 <- mRMR.ensemble(data = mRMR.data(tmp), solution_count=5, target_indices = 1, feature_count = 300, method='bootstrap')\n",
    "res_class1 <- mRMR.ensemble(data = mRMR.data(tmp), solution_count=1, target_indices = 1, feature_count = 300, method='exhaustive')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th></th><th scope=col>target</th><th scope=col>A</th><th scope=col>C</th><th scope=col>G</th><th scope=col>T</th><th scope=col>Total</th><th scope=col>AA</th><th scope=col>AC</th><th scope=col>AT</th><th scope=col>AG</th><th scope=col>⋯</th><th scope=col>GGCT</th><th scope=col>GGCG</th><th scope=col>GGTA</th><th scope=col>GGTC</th><th scope=col>GGTT</th><th scope=col>GGTG</th><th scope=col>GGGA</th><th scope=col>GGGC</th><th scope=col>GGGT</th><th scope=col>GGGG</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>592</th><td>1          </td><td>0.152897806</td><td>0.125247590</td><td>0.164673480</td><td>0.165089380</td><td>0.173614707</td><td>0.090282295</td><td>0.140238823</td><td>0.150870798</td><td>0.15923222 </td><td>⋯          </td><td>0.079754601</td><td>0.060526316</td><td>0.20238095 </td><td>0.09259259 </td><td>0.18303571 </td><td>0.15151515 </td><td>0.16759777 </td><td>0.13541667 </td><td>0.17647059 </td><td>0.12550607 </td></tr>\n",
       "\t<tr><th scope=row>593</th><td>1          </td><td>0.018976249</td><td>0.012940710</td><td>0.019641951</td><td>0.019321767</td><td>0.019438485</td><td>0.010277091</td><td>0.017772841</td><td>0.021263670</td><td>0.01892403 </td><td>⋯          </td><td>0.006134969</td><td>0.000000000</td><td>0.04166667 </td><td>0.00617284 </td><td>0.03125000 </td><td>0.02651515 </td><td>0.03910615 </td><td>0.02083333 </td><td>0.04575163 </td><td>0.02834008 </td></tr>\n",
       "\t<tr><th scope=row>595</th><td>1          </td><td>0.133861123</td><td>0.104119900</td><td>0.142132348</td><td>0.141824395</td><td>0.145871865</td><td>0.078964485</td><td>0.113857262</td><td>0.139327663</td><td>0.13868613 </td><td>⋯          </td><td>0.085889571</td><td>0.036842105</td><td>0.20833333 </td><td>0.08333333 </td><td>0.20089286 </td><td>0.12878788 </td><td>0.21229050 </td><td>0.11458333 </td><td>0.24836601 </td><td>0.10121457 </td></tr>\n",
       "\t<tr><th scope=row>596</th><td>1          </td><td>0.026470055</td><td>0.026145517</td><td>0.029354207</td><td>0.032137224</td><td>0.031515869</td><td>0.013659425</td><td>0.028325465</td><td>0.028554070</td><td>0.02514193 </td><td>⋯          </td><td>0.000000000</td><td>0.007894737</td><td>0.05952381 </td><td>0.01543210 </td><td>0.03125000 </td><td>0.02651515 </td><td>0.03351955 </td><td>0.04166667 </td><td>0.03267974 </td><td>0.04453441 </td></tr>\n",
       "\t<tr><th scope=row>597</th><td>1          </td><td>0.003202998</td><td>0.003499274</td><td>0.002246865</td><td>0.006834911</td><td>0.004013465</td><td>0.001300898</td><td>0.003054707</td><td>0.005467801</td><td>0.00243309 </td><td>⋯          </td><td>0.000000000</td><td>0.000000000</td><td>0.00000000 </td><td>0.00308642 </td><td>0.01339286 </td><td>0.00000000 </td><td>0.00000000 </td><td>0.00000000 </td><td>0.00000000 </td><td>0.00000000 </td></tr>\n",
       "\t<tr><th scope=row>598</th><td>1          </td><td>0.148909168</td><td>0.107223029</td><td>0.144016815</td><td>0.161277603</td><td>0.157301916</td><td>0.087940679</td><td>0.128575396</td><td>0.155123532</td><td>0.15193295 </td><td>⋯          </td><td>0.042944785</td><td>0.034210526</td><td>0.19047619 </td><td>0.06481481 </td><td>0.15178571 </td><td>0.14015152 </td><td>0.19553073 </td><td>0.08854167 </td><td>0.16993464 </td><td>0.07692308 </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|llllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllll}\n",
       "  & target & A & C & G & T & Total & AA & AC & AT & AG & ⋯ & GGCT & GGCG & GGTA & GGTC & GGTT & GGTG & GGGA & GGGC & GGGT & GGGG\\\\\n",
       "\\hline\n",
       "\t592 & 1           & 0.152897806 & 0.125247590 & 0.164673480 & 0.165089380 & 0.173614707 & 0.090282295 & 0.140238823 & 0.150870798 & 0.15923222  & ⋯           & 0.079754601 & 0.060526316 & 0.20238095  & 0.09259259  & 0.18303571  & 0.15151515  & 0.16759777  & 0.13541667  & 0.17647059  & 0.12550607 \\\\\n",
       "\t593 & 1           & 0.018976249 & 0.012940710 & 0.019641951 & 0.019321767 & 0.019438485 & 0.010277091 & 0.017772841 & 0.021263670 & 0.01892403  & ⋯           & 0.006134969 & 0.000000000 & 0.04166667  & 0.00617284  & 0.03125000  & 0.02651515  & 0.03910615  & 0.02083333  & 0.04575163  & 0.02834008 \\\\\n",
       "\t595 & 1           & 0.133861123 & 0.104119900 & 0.142132348 & 0.141824395 & 0.145871865 & 0.078964485 & 0.113857262 & 0.139327663 & 0.13868613  & ⋯           & 0.085889571 & 0.036842105 & 0.20833333  & 0.08333333  & 0.20089286  & 0.12878788  & 0.21229050  & 0.11458333  & 0.24836601  & 0.10121457 \\\\\n",
       "\t596 & 1           & 0.026470055 & 0.026145517 & 0.029354207 & 0.032137224 & 0.031515869 & 0.013659425 & 0.028325465 & 0.028554070 & 0.02514193  & ⋯           & 0.000000000 & 0.007894737 & 0.05952381  & 0.01543210  & 0.03125000  & 0.02651515  & 0.03351955  & 0.04166667  & 0.03267974  & 0.04453441 \\\\\n",
       "\t597 & 1           & 0.003202998 & 0.003499274 & 0.002246865 & 0.006834911 & 0.004013465 & 0.001300898 & 0.003054707 & 0.005467801 & 0.00243309  & ⋯           & 0.000000000 & 0.000000000 & 0.00000000  & 0.00308642  & 0.01339286  & 0.00000000  & 0.00000000  & 0.00000000  & 0.00000000  & 0.00000000 \\\\\n",
       "\t598 & 1           & 0.148909168 & 0.107223029 & 0.144016815 & 0.161277603 & 0.157301916 & 0.087940679 & 0.128575396 & 0.155123532 & 0.15193295  & ⋯           & 0.042944785 & 0.034210526 & 0.19047619  & 0.06481481  & 0.15178571  & 0.14015152  & 0.19553073  & 0.08854167  & 0.16993464  & 0.07692308 \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "| <!--/--> | target | A | C | G | T | Total | AA | AC | AT | AG | ⋯ | GGCT | GGCG | GGTA | GGTC | GGTT | GGTG | GGGA | GGGC | GGGT | GGGG | \n",
       "|---|---|---|---|---|---|\n",
       "| 592 | 1           | 0.152897806 | 0.125247590 | 0.164673480 | 0.165089380 | 0.173614707 | 0.090282295 | 0.140238823 | 0.150870798 | 0.15923222  | ⋯           | 0.079754601 | 0.060526316 | 0.20238095  | 0.09259259  | 0.18303571  | 0.15151515  | 0.16759777  | 0.13541667  | 0.17647059  | 0.12550607  | \n",
       "| 593 | 1           | 0.018976249 | 0.012940710 | 0.019641951 | 0.019321767 | 0.019438485 | 0.010277091 | 0.017772841 | 0.021263670 | 0.01892403  | ⋯           | 0.006134969 | 0.000000000 | 0.04166667  | 0.00617284  | 0.03125000  | 0.02651515  | 0.03910615  | 0.02083333  | 0.04575163  | 0.02834008  | \n",
       "| 595 | 1           | 0.133861123 | 0.104119900 | 0.142132348 | 0.141824395 | 0.145871865 | 0.078964485 | 0.113857262 | 0.139327663 | 0.13868613  | ⋯           | 0.085889571 | 0.036842105 | 0.20833333  | 0.08333333  | 0.20089286  | 0.12878788  | 0.21229050  | 0.11458333  | 0.24836601  | 0.10121457  | \n",
       "| 596 | 1           | 0.026470055 | 0.026145517 | 0.029354207 | 0.032137224 | 0.031515869 | 0.013659425 | 0.028325465 | 0.028554070 | 0.02514193  | ⋯           | 0.000000000 | 0.007894737 | 0.05952381  | 0.01543210  | 0.03125000  | 0.02651515  | 0.03351955  | 0.04166667  | 0.03267974  | 0.04453441  | \n",
       "| 597 | 1           | 0.003202998 | 0.003499274 | 0.002246865 | 0.006834911 | 0.004013465 | 0.001300898 | 0.003054707 | 0.005467801 | 0.00243309  | ⋯           | 0.000000000 | 0.000000000 | 0.00000000  | 0.00308642  | 0.01339286  | 0.00000000  | 0.00000000  | 0.00000000  | 0.00000000  | 0.00000000  | \n",
       "| 598 | 1           | 0.148909168 | 0.107223029 | 0.144016815 | 0.161277603 | 0.157301916 | 0.087940679 | 0.128575396 | 0.155123532 | 0.15193295  | ⋯           | 0.042944785 | 0.034210526 | 0.19047619  | 0.06481481  | 0.15178571  | 0.14015152  | 0.19553073  | 0.08854167  | 0.16993464  | 0.07692308  | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "    target A           C           G           T           Total      \n",
       "592 1      0.152897806 0.125247590 0.164673480 0.165089380 0.173614707\n",
       "593 1      0.018976249 0.012940710 0.019641951 0.019321767 0.019438485\n",
       "595 1      0.133861123 0.104119900 0.142132348 0.141824395 0.145871865\n",
       "596 1      0.026470055 0.026145517 0.029354207 0.032137224 0.031515869\n",
       "597 1      0.003202998 0.003499274 0.002246865 0.006834911 0.004013465\n",
       "598 1      0.148909168 0.107223029 0.144016815 0.161277603 0.157301916\n",
       "    AA          AC          AT          AG         ⋯ GGCT        GGCG       \n",
       "592 0.090282295 0.140238823 0.150870798 0.15923222 ⋯ 0.079754601 0.060526316\n",
       "593 0.010277091 0.017772841 0.021263670 0.01892403 ⋯ 0.006134969 0.000000000\n",
       "595 0.078964485 0.113857262 0.139327663 0.13868613 ⋯ 0.085889571 0.036842105\n",
       "596 0.013659425 0.028325465 0.028554070 0.02514193 ⋯ 0.000000000 0.007894737\n",
       "597 0.001300898 0.003054707 0.005467801 0.00243309 ⋯ 0.000000000 0.000000000\n",
       "598 0.087940679 0.128575396 0.155123532 0.15193295 ⋯ 0.042944785 0.034210526\n",
       "    GGTA       GGTC       GGTT       GGTG       GGGA       GGGC      \n",
       "592 0.20238095 0.09259259 0.18303571 0.15151515 0.16759777 0.13541667\n",
       "593 0.04166667 0.00617284 0.03125000 0.02651515 0.03910615 0.02083333\n",
       "595 0.20833333 0.08333333 0.20089286 0.12878788 0.21229050 0.11458333\n",
       "596 0.05952381 0.01543210 0.03125000 0.02651515 0.03351955 0.04166667\n",
       "597 0.00000000 0.00308642 0.01339286 0.00000000 0.00000000 0.00000000\n",
       "598 0.19047619 0.06481481 0.15178571 0.14015152 0.19553073 0.08854167\n",
       "    GGGT       GGGG      \n",
       "592 0.17647059 0.12550607\n",
       "593 0.04575163 0.02834008\n",
       "595 0.24836601 0.10121457\n",
       "596 0.03267974 0.04453441\n",
       "597 0.00000000 0.00000000\n",
       "598 0.16993464 0.07692308"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Class 1, Order LTR node features\n",
    "indx <- target[,1]==1 & target[,2]==1 & !is.na(target[,3]) # Those in class 1, order LTR with known superfamily\n",
    "tmp <- cbind(target[indx,3],data[indx,])\n",
    "names(tmp)[1] <- 'target'\n",
    "head(tmp)\n",
    "# res_class1orderLTR <- mRMR.ensemble(data = mRMR.data(tmp), solution_count=5, target_indices = 1, feature_count = 300, method='bootstrap')\n",
    "res_class1orderLTR <- mRMR.ensemble(data = mRMR.data(tmp), solution_count=1, target_indices = 1, feature_count = 300, method='exhaustive')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "integer(0)\n"
     ]
    }
   ],
   "source": [
    "# Class 1, Order DIRS node features\n",
    "indx <- target[,1]==1 & target[,2]==2 & !is.na(target[,3]) # Those in class 1, order DIRS with known superfamily\n",
    "print(which(indx))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th></th><th scope=col>target</th><th scope=col>A</th><th scope=col>C</th><th scope=col>G</th><th scope=col>T</th><th scope=col>Total</th><th scope=col>AA</th><th scope=col>AC</th><th scope=col>AT</th><th scope=col>AG</th><th scope=col>⋯</th><th scope=col>GGCT</th><th scope=col>GGCG</th><th scope=col>GGTA</th><th scope=col>GGTC</th><th scope=col>GGTT</th><th scope=col>GGTG</th><th scope=col>GGGA</th><th scope=col>GGGC</th><th scope=col>GGGT</th><th scope=col>GGGG</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>14163</th><td>3          </td><td>0.07318547 </td><td>0.08933052 </td><td>0.06921795 </td><td>0.05336488 </td><td>0.07965895 </td><td>0.05021465 </td><td>0.09414052 </td><td>0.03746456 </td><td>0.08218437 </td><td>⋯          </td><td>0.08588957 </td><td>0.015789474</td><td>0.05357143 </td><td>0.02777778 </td><td>0.040178571</td><td>0.026515152</td><td>0.067039106</td><td>0.015625000</td><td>0.03921569 </td><td>0.032388664</td></tr>\n",
       "\t<tr><th scope=row>14164</th><td>3          </td><td>0.11832961 </td><td>0.07335270 </td><td>0.05595419 </td><td>0.08983964 </td><td>0.09587926 </td><td>0.09665669 </td><td>0.11607887 </td><td>0.10348319 </td><td>0.07812922 </td><td>⋯          </td><td>0.02453988 </td><td>0.005263158</td><td>0.04166667 </td><td>0.02469136 </td><td>0.031250000</td><td>0.049242424</td><td>0.011173184</td><td>0.005208333</td><td>0.03921569 </td><td>0.012145749</td></tr>\n",
       "\t<tr><th scope=row>14165</th><td>3          </td><td>0.07868496 </td><td>0.06298693 </td><td>0.06139016 </td><td>0.05789958 </td><td>0.07333358 </td><td>0.05619878 </td><td>0.08275479 </td><td>0.05913325 </td><td>0.07542579 </td><td>⋯          </td><td>0.11042945 </td><td>0.010526316</td><td>0.08928571 </td><td>0.02160494 </td><td>0.044642857</td><td>0.037878788</td><td>0.078212291</td><td>0.036458333</td><td>0.01960784 </td><td>0.028340081</td></tr>\n",
       "\t<tr><th scope=row>14166</th><td>3          </td><td>0.02495921 </td><td>0.02000528 </td><td>0.01891716 </td><td>0.02122766 </td><td>0.02363690 </td><td>0.01639131 </td><td>0.02582616 </td><td>0.02369380 </td><td>0.02189781 </td><td>⋯          </td><td>0.03067485 </td><td>0.000000000</td><td>0.01190476 </td><td>0.00617284 </td><td>0.008928571</td><td>0.022727273</td><td>0.033519553</td><td>0.010416667</td><td>0.00000000 </td><td>0.004048583</td></tr>\n",
       "\t<tr><th scope=row>14167</th><td>3          </td><td>0.09814468 </td><td>0.08629341 </td><td>0.05443212 </td><td>0.07761567 </td><td>0.08953540 </td><td>0.08065565 </td><td>0.11441266 </td><td>0.08383961 </td><td>0.04920249 </td><td>⋯          </td><td>0.06748466 </td><td>0.036842105</td><td>0.02976190 </td><td>0.01543210 </td><td>0.026785714</td><td>0.045454545</td><td>0.033519553</td><td>0.046875000</td><td>0.01307190 </td><td>0.032388664</td></tr>\n",
       "\t<tr><th scope=row>14168</th><td>3          </td><td>0.08744788 </td><td>0.08041727 </td><td>0.04696673 </td><td>0.06690326 </td><td>0.07967744 </td><td>0.06504488 </td><td>0.10413774 </td><td>0.07999190 </td><td>0.04866180 </td><td>⋯          </td><td>0.06134969 </td><td>0.010526316</td><td>0.01785714 </td><td>0.00308642 </td><td>0.017857143</td><td>0.007575758</td><td>0.005586592</td><td>0.015625000</td><td>0.01960784 </td><td>0.000000000</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|llllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllll}\n",
       "  & target & A & C & G & T & Total & AA & AC & AT & AG & ⋯ & GGCT & GGCG & GGTA & GGTC & GGTT & GGTG & GGGA & GGGC & GGGT & GGGG\\\\\n",
       "\\hline\n",
       "\t14163 & 3           & 0.07318547  & 0.08933052  & 0.06921795  & 0.05336488  & 0.07965895  & 0.05021465  & 0.09414052  & 0.03746456  & 0.08218437  & ⋯           & 0.08588957  & 0.015789474 & 0.05357143  & 0.02777778  & 0.040178571 & 0.026515152 & 0.067039106 & 0.015625000 & 0.03921569  & 0.032388664\\\\\n",
       "\t14164 & 3           & 0.11832961  & 0.07335270  & 0.05595419  & 0.08983964  & 0.09587926  & 0.09665669  & 0.11607887  & 0.10348319  & 0.07812922  & ⋯           & 0.02453988  & 0.005263158 & 0.04166667  & 0.02469136  & 0.031250000 & 0.049242424 & 0.011173184 & 0.005208333 & 0.03921569  & 0.012145749\\\\\n",
       "\t14165 & 3           & 0.07868496  & 0.06298693  & 0.06139016  & 0.05789958  & 0.07333358  & 0.05619878  & 0.08275479  & 0.05913325  & 0.07542579  & ⋯           & 0.11042945  & 0.010526316 & 0.08928571  & 0.02160494  & 0.044642857 & 0.037878788 & 0.078212291 & 0.036458333 & 0.01960784  & 0.028340081\\\\\n",
       "\t14166 & 3           & 0.02495921  & 0.02000528  & 0.01891716  & 0.02122766  & 0.02363690  & 0.01639131  & 0.02582616  & 0.02369380  & 0.02189781  & ⋯           & 0.03067485  & 0.000000000 & 0.01190476  & 0.00617284  & 0.008928571 & 0.022727273 & 0.033519553 & 0.010416667 & 0.00000000  & 0.004048583\\\\\n",
       "\t14167 & 3           & 0.09814468  & 0.08629341  & 0.05443212  & 0.07761567  & 0.08953540  & 0.08065565  & 0.11441266  & 0.08383961  & 0.04920249  & ⋯           & 0.06748466  & 0.036842105 & 0.02976190  & 0.01543210  & 0.026785714 & 0.045454545 & 0.033519553 & 0.046875000 & 0.01307190  & 0.032388664\\\\\n",
       "\t14168 & 3           & 0.08744788  & 0.08041727  & 0.04696673  & 0.06690326  & 0.07967744  & 0.06504488  & 0.10413774  & 0.07999190  & 0.04866180  & ⋯           & 0.06134969  & 0.010526316 & 0.01785714  & 0.00308642  & 0.017857143 & 0.007575758 & 0.005586592 & 0.015625000 & 0.01960784  & 0.000000000\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "| <!--/--> | target | A | C | G | T | Total | AA | AC | AT | AG | ⋯ | GGCT | GGCG | GGTA | GGTC | GGTT | GGTG | GGGA | GGGC | GGGT | GGGG | \n",
       "|---|---|---|---|---|---|\n",
       "| 14163 | 3           | 0.07318547  | 0.08933052  | 0.06921795  | 0.05336488  | 0.07965895  | 0.05021465  | 0.09414052  | 0.03746456  | 0.08218437  | ⋯           | 0.08588957  | 0.015789474 | 0.05357143  | 0.02777778  | 0.040178571 | 0.026515152 | 0.067039106 | 0.015625000 | 0.03921569  | 0.032388664 | \n",
       "| 14164 | 3           | 0.11832961  | 0.07335270  | 0.05595419  | 0.08983964  | 0.09587926  | 0.09665669  | 0.11607887  | 0.10348319  | 0.07812922  | ⋯           | 0.02453988  | 0.005263158 | 0.04166667  | 0.02469136  | 0.031250000 | 0.049242424 | 0.011173184 | 0.005208333 | 0.03921569  | 0.012145749 | \n",
       "| 14165 | 3           | 0.07868496  | 0.06298693  | 0.06139016  | 0.05789958  | 0.07333358  | 0.05619878  | 0.08275479  | 0.05913325  | 0.07542579  | ⋯           | 0.11042945  | 0.010526316 | 0.08928571  | 0.02160494  | 0.044642857 | 0.037878788 | 0.078212291 | 0.036458333 | 0.01960784  | 0.028340081 | \n",
       "| 14166 | 3           | 0.02495921  | 0.02000528  | 0.01891716  | 0.02122766  | 0.02363690  | 0.01639131  | 0.02582616  | 0.02369380  | 0.02189781  | ⋯           | 0.03067485  | 0.000000000 | 0.01190476  | 0.00617284  | 0.008928571 | 0.022727273 | 0.033519553 | 0.010416667 | 0.00000000  | 0.004048583 | \n",
       "| 14167 | 3           | 0.09814468  | 0.08629341  | 0.05443212  | 0.07761567  | 0.08953540  | 0.08065565  | 0.11441266  | 0.08383961  | 0.04920249  | ⋯           | 0.06748466  | 0.036842105 | 0.02976190  | 0.01543210  | 0.026785714 | 0.045454545 | 0.033519553 | 0.046875000 | 0.01307190  | 0.032388664 | \n",
       "| 14168 | 3           | 0.08744788  | 0.08041727  | 0.04696673  | 0.06690326  | 0.07967744  | 0.06504488  | 0.10413774  | 0.07999190  | 0.04866180  | ⋯           | 0.06134969  | 0.010526316 | 0.01785714  | 0.00308642  | 0.017857143 | 0.007575758 | 0.005586592 | 0.015625000 | 0.01960784  | 0.000000000 | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "      target A          C          G          T          Total      AA        \n",
       "14163 3      0.07318547 0.08933052 0.06921795 0.05336488 0.07965895 0.05021465\n",
       "14164 3      0.11832961 0.07335270 0.05595419 0.08983964 0.09587926 0.09665669\n",
       "14165 3      0.07868496 0.06298693 0.06139016 0.05789958 0.07333358 0.05619878\n",
       "14166 3      0.02495921 0.02000528 0.01891716 0.02122766 0.02363690 0.01639131\n",
       "14167 3      0.09814468 0.08629341 0.05443212 0.07761567 0.08953540 0.08065565\n",
       "14168 3      0.08744788 0.08041727 0.04696673 0.06690326 0.07967744 0.06504488\n",
       "      AC         AT         AG         ⋯ GGCT       GGCG        GGTA      \n",
       "14163 0.09414052 0.03746456 0.08218437 ⋯ 0.08588957 0.015789474 0.05357143\n",
       "14164 0.11607887 0.10348319 0.07812922 ⋯ 0.02453988 0.005263158 0.04166667\n",
       "14165 0.08275479 0.05913325 0.07542579 ⋯ 0.11042945 0.010526316 0.08928571\n",
       "14166 0.02582616 0.02369380 0.02189781 ⋯ 0.03067485 0.000000000 0.01190476\n",
       "14167 0.11441266 0.08383961 0.04920249 ⋯ 0.06748466 0.036842105 0.02976190\n",
       "14168 0.10413774 0.07999190 0.04866180 ⋯ 0.06134969 0.010526316 0.01785714\n",
       "      GGTC       GGTT        GGTG        GGGA        GGGC        GGGT      \n",
       "14163 0.02777778 0.040178571 0.026515152 0.067039106 0.015625000 0.03921569\n",
       "14164 0.02469136 0.031250000 0.049242424 0.011173184 0.005208333 0.03921569\n",
       "14165 0.02160494 0.044642857 0.037878788 0.078212291 0.036458333 0.01960784\n",
       "14166 0.00617284 0.008928571 0.022727273 0.033519553 0.010416667 0.00000000\n",
       "14167 0.01543210 0.026785714 0.045454545 0.033519553 0.046875000 0.01307190\n",
       "14168 0.00308642 0.017857143 0.007575758 0.005586592 0.015625000 0.01960784\n",
       "      GGGG       \n",
       "14163 0.032388664\n",
       "14164 0.012145749\n",
       "14165 0.028340081\n",
       "14166 0.004048583\n",
       "14167 0.032388664\n",
       "14168 0.000000000"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Class 1, Order LINE node features\n",
    "indx <- target[,1]==1 & target[,2]==4 & !is.na(target[,3]) # Those in class 1, order LINE with known superfamily\n",
    "tmp <- cbind(target[indx,3],data[indx,])\n",
    "names(tmp)[1] <- 'target'\n",
    "head(tmp)\n",
    "# res_class1orderLINE <- mRMR.ensemble(data = mRMR.data(tmp), solution_count=5, target_indices = 1, feature_count = 300, method='bootstrap')\n",
    "res_class1orderLINE <- mRMR.ensemble(data = mRMR.data(tmp), solution_count=1, target_indices = 1, feature_count = 300, method='exhaustive')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th></th><th scope=col>target</th><th scope=col>A</th><th scope=col>C</th><th scope=col>G</th><th scope=col>T</th><th scope=col>Total</th><th scope=col>AA</th><th scope=col>AC</th><th scope=col>AT</th><th scope=col>AG</th><th scope=col>⋯</th><th scope=col>GGCT</th><th scope=col>GGCG</th><th scope=col>GGTA</th><th scope=col>GGTC</th><th scope=col>GGTT</th><th scope=col>GGTG</th><th scope=col>GGGA</th><th scope=col>GGGC</th><th scope=col>GGGT</th><th scope=col>GGGG</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>14355</th><td>3          </td><td>0.004774279</td><td>0.006140235</td><td>0.006813075</td><td>0.004403260</td><td>0.005715026</td><td>0.002731885</td><td>0.006664815</td><td>0.003240178</td><td>0.005947553</td><td>⋯          </td><td>0.018404908</td><td>0.005263158</td><td>0.011904762</td><td>0.00308642 </td><td>0.004464286</td><td>0.007575758</td><td>0.022346369</td><td>0.005208333</td><td>0.013071895</td><td>0.004048583</td></tr>\n",
       "\t<tr><th scope=row>14356</th><td>1          </td><td>0.006829032</td><td>0.007064572</td><td>0.009567297</td><td>0.006966351</td><td>0.008045424</td><td>0.005073501</td><td>0.004998611</td><td>0.004455245</td><td>0.009732360</td><td>⋯          </td><td>0.018404908</td><td>0.005263158</td><td>0.005952381</td><td>0.00000000 </td><td>0.008928571</td><td>0.011363636</td><td>0.016759777</td><td>0.010416667</td><td>0.013071895</td><td>0.012145749</td></tr>\n",
       "\t<tr><th scope=row>14363</th><td>1          </td><td>0.002477791</td><td>0.002971081</td><td>0.004421251</td><td>0.003680336</td><td>0.003310646</td><td>0.001821257</td><td>0.002499306</td><td>0.001417578</td><td>0.004055150</td><td>⋯          </td><td>0.006134969</td><td>0.002631579</td><td>0.000000000</td><td>0.00617284 </td><td>0.017857143</td><td>0.003787879</td><td>0.005586592</td><td>0.005208333</td><td>0.013071895</td><td>0.004048583</td></tr>\n",
       "\t<tr><th scope=row>14364</th><td>1          </td><td>0.003142564</td><td>0.003433250</td><td>0.003696456</td><td>0.002300210</td><td>0.003070208</td><td>0.002341616</td><td>0.004720911</td><td>0.001215067</td><td>0.003784807</td><td>⋯          </td><td>0.000000000</td><td>0.005263158</td><td>0.000000000</td><td>0.00617284 </td><td>0.013392857</td><td>0.007575758</td><td>0.000000000</td><td>0.000000000</td><td>0.013071895</td><td>0.004048583</td></tr>\n",
       "\t<tr><th scope=row>14365</th><td>1          </td><td>0.002115187</td><td>0.002574937</td><td>0.004276292</td><td>0.002431651</td><td>0.002700303</td><td>0.001561077</td><td>0.002221605</td><td>0.001215067</td><td>0.003514463</td><td>⋯          </td><td>0.006134969</td><td>0.005263158</td><td>0.000000000</td><td>0.00617284 </td><td>0.017857143</td><td>0.003787879</td><td>0.005586592</td><td>0.000000000</td><td>0.013071895</td><td>0.004048583</td></tr>\n",
       "\t<tr><th scope=row>14366</th><td>1          </td><td>0.002900828</td><td>0.003829394</td><td>0.003986374</td><td>0.002037329</td><td>0.003107198</td><td>0.002341616</td><td>0.004443210</td><td>0.001215067</td><td>0.002973777</td><td>⋯          </td><td>0.012269939</td><td>0.007894737</td><td>0.000000000</td><td>0.00308642 </td><td>0.013392857</td><td>0.003787879</td><td>0.005586592</td><td>0.005208333</td><td>0.006535948</td><td>0.008097166</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|llllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllll}\n",
       "  & target & A & C & G & T & Total & AA & AC & AT & AG & ⋯ & GGCT & GGCG & GGTA & GGTC & GGTT & GGTG & GGGA & GGGC & GGGT & GGGG\\\\\n",
       "\\hline\n",
       "\t14355 & 3           & 0.004774279 & 0.006140235 & 0.006813075 & 0.004403260 & 0.005715026 & 0.002731885 & 0.006664815 & 0.003240178 & 0.005947553 & ⋯           & 0.018404908 & 0.005263158 & 0.011904762 & 0.00308642  & 0.004464286 & 0.007575758 & 0.022346369 & 0.005208333 & 0.013071895 & 0.004048583\\\\\n",
       "\t14356 & 1           & 0.006829032 & 0.007064572 & 0.009567297 & 0.006966351 & 0.008045424 & 0.005073501 & 0.004998611 & 0.004455245 & 0.009732360 & ⋯           & 0.018404908 & 0.005263158 & 0.005952381 & 0.00000000  & 0.008928571 & 0.011363636 & 0.016759777 & 0.010416667 & 0.013071895 & 0.012145749\\\\\n",
       "\t14363 & 1           & 0.002477791 & 0.002971081 & 0.004421251 & 0.003680336 & 0.003310646 & 0.001821257 & 0.002499306 & 0.001417578 & 0.004055150 & ⋯           & 0.006134969 & 0.002631579 & 0.000000000 & 0.00617284  & 0.017857143 & 0.003787879 & 0.005586592 & 0.005208333 & 0.013071895 & 0.004048583\\\\\n",
       "\t14364 & 1           & 0.003142564 & 0.003433250 & 0.003696456 & 0.002300210 & 0.003070208 & 0.002341616 & 0.004720911 & 0.001215067 & 0.003784807 & ⋯           & 0.000000000 & 0.005263158 & 0.000000000 & 0.00617284  & 0.013392857 & 0.007575758 & 0.000000000 & 0.000000000 & 0.013071895 & 0.004048583\\\\\n",
       "\t14365 & 1           & 0.002115187 & 0.002574937 & 0.004276292 & 0.002431651 & 0.002700303 & 0.001561077 & 0.002221605 & 0.001215067 & 0.003514463 & ⋯           & 0.006134969 & 0.005263158 & 0.000000000 & 0.00617284  & 0.017857143 & 0.003787879 & 0.005586592 & 0.000000000 & 0.013071895 & 0.004048583\\\\\n",
       "\t14366 & 1           & 0.002900828 & 0.003829394 & 0.003986374 & 0.002037329 & 0.003107198 & 0.002341616 & 0.004443210 & 0.001215067 & 0.002973777 & ⋯           & 0.012269939 & 0.007894737 & 0.000000000 & 0.00308642  & 0.013392857 & 0.003787879 & 0.005586592 & 0.005208333 & 0.006535948 & 0.008097166\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "| <!--/--> | target | A | C | G | T | Total | AA | AC | AT | AG | ⋯ | GGCT | GGCG | GGTA | GGTC | GGTT | GGTG | GGGA | GGGC | GGGT | GGGG | \n",
       "|---|---|---|---|---|---|\n",
       "| 14355 | 3           | 0.004774279 | 0.006140235 | 0.006813075 | 0.004403260 | 0.005715026 | 0.002731885 | 0.006664815 | 0.003240178 | 0.005947553 | ⋯           | 0.018404908 | 0.005263158 | 0.011904762 | 0.00308642  | 0.004464286 | 0.007575758 | 0.022346369 | 0.005208333 | 0.013071895 | 0.004048583 | \n",
       "| 14356 | 1           | 0.006829032 | 0.007064572 | 0.009567297 | 0.006966351 | 0.008045424 | 0.005073501 | 0.004998611 | 0.004455245 | 0.009732360 | ⋯           | 0.018404908 | 0.005263158 | 0.005952381 | 0.00000000  | 0.008928571 | 0.011363636 | 0.016759777 | 0.010416667 | 0.013071895 | 0.012145749 | \n",
       "| 14363 | 1           | 0.002477791 | 0.002971081 | 0.004421251 | 0.003680336 | 0.003310646 | 0.001821257 | 0.002499306 | 0.001417578 | 0.004055150 | ⋯           | 0.006134969 | 0.002631579 | 0.000000000 | 0.00617284  | 0.017857143 | 0.003787879 | 0.005586592 | 0.005208333 | 0.013071895 | 0.004048583 | \n",
       "| 14364 | 1           | 0.003142564 | 0.003433250 | 0.003696456 | 0.002300210 | 0.003070208 | 0.002341616 | 0.004720911 | 0.001215067 | 0.003784807 | ⋯           | 0.000000000 | 0.005263158 | 0.000000000 | 0.00617284  | 0.013392857 | 0.007575758 | 0.000000000 | 0.000000000 | 0.013071895 | 0.004048583 | \n",
       "| 14365 | 1           | 0.002115187 | 0.002574937 | 0.004276292 | 0.002431651 | 0.002700303 | 0.001561077 | 0.002221605 | 0.001215067 | 0.003514463 | ⋯           | 0.006134969 | 0.005263158 | 0.000000000 | 0.00617284  | 0.017857143 | 0.003787879 | 0.005586592 | 0.000000000 | 0.013071895 | 0.004048583 | \n",
       "| 14366 | 1           | 0.002900828 | 0.003829394 | 0.003986374 | 0.002037329 | 0.003107198 | 0.002341616 | 0.004443210 | 0.001215067 | 0.002973777 | ⋯           | 0.012269939 | 0.007894737 | 0.000000000 | 0.00308642  | 0.013392857 | 0.003787879 | 0.005586592 | 0.005208333 | 0.006535948 | 0.008097166 | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "      target A           C           G           T           Total      \n",
       "14355 3      0.004774279 0.006140235 0.006813075 0.004403260 0.005715026\n",
       "14356 1      0.006829032 0.007064572 0.009567297 0.006966351 0.008045424\n",
       "14363 1      0.002477791 0.002971081 0.004421251 0.003680336 0.003310646\n",
       "14364 1      0.003142564 0.003433250 0.003696456 0.002300210 0.003070208\n",
       "14365 1      0.002115187 0.002574937 0.004276292 0.002431651 0.002700303\n",
       "14366 1      0.002900828 0.003829394 0.003986374 0.002037329 0.003107198\n",
       "      AA          AC          AT          AG          ⋯ GGCT        GGCG       \n",
       "14355 0.002731885 0.006664815 0.003240178 0.005947553 ⋯ 0.018404908 0.005263158\n",
       "14356 0.005073501 0.004998611 0.004455245 0.009732360 ⋯ 0.018404908 0.005263158\n",
       "14363 0.001821257 0.002499306 0.001417578 0.004055150 ⋯ 0.006134969 0.002631579\n",
       "14364 0.002341616 0.004720911 0.001215067 0.003784807 ⋯ 0.000000000 0.005263158\n",
       "14365 0.001561077 0.002221605 0.001215067 0.003514463 ⋯ 0.006134969 0.005263158\n",
       "14366 0.002341616 0.004443210 0.001215067 0.002973777 ⋯ 0.012269939 0.007894737\n",
       "      GGTA        GGTC       GGTT        GGTG        GGGA        GGGC       \n",
       "14355 0.011904762 0.00308642 0.004464286 0.007575758 0.022346369 0.005208333\n",
       "14356 0.005952381 0.00000000 0.008928571 0.011363636 0.016759777 0.010416667\n",
       "14363 0.000000000 0.00617284 0.017857143 0.003787879 0.005586592 0.005208333\n",
       "14364 0.000000000 0.00617284 0.013392857 0.007575758 0.000000000 0.000000000\n",
       "14365 0.000000000 0.00617284 0.017857143 0.003787879 0.005586592 0.000000000\n",
       "14366 0.000000000 0.00308642 0.013392857 0.003787879 0.005586592 0.005208333\n",
       "      GGGT        GGGG       \n",
       "14355 0.013071895 0.004048583\n",
       "14356 0.013071895 0.012145749\n",
       "14363 0.013071895 0.004048583\n",
       "14364 0.013071895 0.004048583\n",
       "14365 0.013071895 0.004048583\n",
       "14366 0.006535948 0.008097166"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Class 1, Order SINE node features\n",
    "indx <- target[,1]==1 & target[,2]==5 & !is.na(target[,3]) # Those in class 1, order LINE with known superfamily\n",
    "tmp <- cbind(target[indx,3],data[indx,])\n",
    "names(tmp)[1] <- 'target'\n",
    "head(tmp)\n",
    "# res_class1orderSINE <- mRMR.ensemble(data = mRMR.data(tmp), solution_count=5, target_indices = 1, feature_count = 300, method='bootstrap')\n",
    "res_class1orderSINE <- mRMR.ensemble(data = mRMR.data(tmp), solution_count=1, target_indices = 1, feature_count = 300, method='exhaustive')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th></th><th scope=col>target</th><th scope=col>A</th><th scope=col>C</th><th scope=col>G</th><th scope=col>T</th><th scope=col>Total</th><th scope=col>AA</th><th scope=col>AC</th><th scope=col>AT</th><th scope=col>AG</th><th scope=col>⋯</th><th scope=col>GGCT</th><th scope=col>GGCG</th><th scope=col>GGTA</th><th scope=col>GGTC</th><th scope=col>GGTT</th><th scope=col>GGTG</th><th scope=col>GGGA</th><th scope=col>GGGC</th><th scope=col>GGGT</th><th scope=col>GGGG</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>11086</th><td>9           </td><td>0.150843053 </td><td>0.145450944 </td><td>0.159237515 </td><td>0.155757098 </td><td>0.170932899 </td><td>0.0947053467</td><td>0.1624548736</td><td>0.122114216 </td><td>0.15788051  </td><td>⋯           </td><td>0.208588957 </td><td>0.07368421  </td><td>0.154761905 </td><td>0.09567901  </td><td>0.11160714  </td><td>0.200757576 </td><td>0.167597765 </td><td>0.1927083   </td><td>0.18300654  </td><td>0.121457490 </td></tr>\n",
       "\t<tr><th scope=row>11087</th><td>9           </td><td>0.001329546 </td><td>0.002376865 </td><td>0.002536783 </td><td>0.002168770 </td><td>0.001886513 </td><td>0.0006504488</td><td>0.0008331019</td><td>0.002430134 </td><td>0.00162206  </td><td>⋯           </td><td>0.006134969 </td><td>0.00000000  </td><td>0.000000000 </td><td>0.00000000  </td><td>0.00000000  </td><td>0.003787879 </td><td>0.000000000 </td><td>0.0000000   </td><td>0.00000000  </td><td>0.000000000 </td></tr>\n",
       "\t<tr><th scope=row>11088</th><td>9           </td><td>0.007554239 </td><td>0.009045292 </td><td>0.014350946 </td><td>0.008017876 </td><td>0.010320337 </td><td>0.0031221543</td><td>0.0063871147</td><td>0.005872823 </td><td>0.01432820  </td><td>⋯           </td><td>0.018404908 </td><td>0.01842105  </td><td>0.005952381 </td><td>0.00308642  </td><td>0.01339286  </td><td>0.007575758 </td><td>0.027932961 </td><td>0.0312500   </td><td>0.01960784  </td><td>0.008097166 </td></tr>\n",
       "\t<tr><th scope=row>11089</th><td>9           </td><td>0.192663323 </td><td>0.186583917 </td><td>0.215626585 </td><td>0.196832282 </td><td>0.223052452 </td><td>0.1131780929</td><td>0.1949458484</td><td>0.172742001 </td><td>0.20735334  </td><td>⋯           </td><td>0.159509202 </td><td>0.15000000  </td><td>0.190476190 </td><td>0.08641975  </td><td>0.20089286  </td><td>0.212121212 </td><td>0.195530726 </td><td>0.2447917   </td><td>0.22222222  </td><td>0.214574899 </td></tr>\n",
       "\t<tr><th scope=row>11090</th><td>9           </td><td>0.023871397 </td><td>0.032351776 </td><td>0.028194535 </td><td>0.021227655 </td><td>0.029092994 </td><td>0.0141797841</td><td>0.0286031658</td><td>0.019441069 </td><td>0.02460124  </td><td>⋯           </td><td>0.030674847 </td><td>0.03157895  </td><td>0.011904762 </td><td>0.01234568  </td><td>0.02232143  </td><td>0.026515152 </td><td>0.005586592 </td><td>0.0312500   </td><td>0.02614379  </td><td>0.032388664 </td></tr>\n",
       "\t<tr><th scope=row>11091</th><td>9           </td><td>0.124735602 </td><td>0.061204278 </td><td>0.090671885 </td><td>0.122239748 </td><td>0.112413997 </td><td>0.0928840900</td><td>0.0824770897</td><td>0.130619684 </td><td>0.11138145  </td><td>⋯           </td><td>0.073619632 </td><td>0.01315789  </td><td>0.113095238 </td><td>0.02777778  </td><td>0.10714286  </td><td>0.071969697 </td><td>0.089385475 </td><td>0.0468750   </td><td>0.09803922  </td><td>0.028340081 </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|llllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllll}\n",
       "  & target & A & C & G & T & Total & AA & AC & AT & AG & ⋯ & GGCT & GGCG & GGTA & GGTC & GGTT & GGTG & GGGA & GGGC & GGGT & GGGG\\\\\n",
       "\\hline\n",
       "\t11086 & 9            & 0.150843053  & 0.145450944  & 0.159237515  & 0.155757098  & 0.170932899  & 0.0947053467 & 0.1624548736 & 0.122114216  & 0.15788051   & ⋯            & 0.208588957  & 0.07368421   & 0.154761905  & 0.09567901   & 0.11160714   & 0.200757576  & 0.167597765  & 0.1927083    & 0.18300654   & 0.121457490 \\\\\n",
       "\t11087 & 9            & 0.001329546  & 0.002376865  & 0.002536783  & 0.002168770  & 0.001886513  & 0.0006504488 & 0.0008331019 & 0.002430134  & 0.00162206   & ⋯            & 0.006134969  & 0.00000000   & 0.000000000  & 0.00000000   & 0.00000000   & 0.003787879  & 0.000000000  & 0.0000000    & 0.00000000   & 0.000000000 \\\\\n",
       "\t11088 & 9            & 0.007554239  & 0.009045292  & 0.014350946  & 0.008017876  & 0.010320337  & 0.0031221543 & 0.0063871147 & 0.005872823  & 0.01432820   & ⋯            & 0.018404908  & 0.01842105   & 0.005952381  & 0.00308642   & 0.01339286   & 0.007575758  & 0.027932961  & 0.0312500    & 0.01960784   & 0.008097166 \\\\\n",
       "\t11089 & 9            & 0.192663323  & 0.186583917  & 0.215626585  & 0.196832282  & 0.223052452  & 0.1131780929 & 0.1949458484 & 0.172742001  & 0.20735334   & ⋯            & 0.159509202  & 0.15000000   & 0.190476190  & 0.08641975   & 0.20089286   & 0.212121212  & 0.195530726  & 0.2447917    & 0.22222222   & 0.214574899 \\\\\n",
       "\t11090 & 9            & 0.023871397  & 0.032351776  & 0.028194535  & 0.021227655  & 0.029092994  & 0.0141797841 & 0.0286031658 & 0.019441069  & 0.02460124   & ⋯            & 0.030674847  & 0.03157895   & 0.011904762  & 0.01234568   & 0.02232143   & 0.026515152  & 0.005586592  & 0.0312500    & 0.02614379   & 0.032388664 \\\\\n",
       "\t11091 & 9            & 0.124735602  & 0.061204278  & 0.090671885  & 0.122239748  & 0.112413997  & 0.0928840900 & 0.0824770897 & 0.130619684  & 0.11138145   & ⋯            & 0.073619632  & 0.01315789   & 0.113095238  & 0.02777778   & 0.10714286   & 0.071969697  & 0.089385475  & 0.0468750    & 0.09803922   & 0.028340081 \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "| <!--/--> | target | A | C | G | T | Total | AA | AC | AT | AG | ⋯ | GGCT | GGCG | GGTA | GGTC | GGTT | GGTG | GGGA | GGGC | GGGT | GGGG | \n",
       "|---|---|---|---|---|---|\n",
       "| 11086 | 9            | 0.150843053  | 0.145450944  | 0.159237515  | 0.155757098  | 0.170932899  | 0.0947053467 | 0.1624548736 | 0.122114216  | 0.15788051   | ⋯            | 0.208588957  | 0.07368421   | 0.154761905  | 0.09567901   | 0.11160714   | 0.200757576  | 0.167597765  | 0.1927083    | 0.18300654   | 0.121457490  | \n",
       "| 11087 | 9            | 0.001329546  | 0.002376865  | 0.002536783  | 0.002168770  | 0.001886513  | 0.0006504488 | 0.0008331019 | 0.002430134  | 0.00162206   | ⋯            | 0.006134969  | 0.00000000   | 0.000000000  | 0.00000000   | 0.00000000   | 0.003787879  | 0.000000000  | 0.0000000    | 0.00000000   | 0.000000000  | \n",
       "| 11088 | 9            | 0.007554239  | 0.009045292  | 0.014350946  | 0.008017876  | 0.010320337  | 0.0031221543 | 0.0063871147 | 0.005872823  | 0.01432820   | ⋯            | 0.018404908  | 0.01842105   | 0.005952381  | 0.00308642   | 0.01339286   | 0.007575758  | 0.027932961  | 0.0312500    | 0.01960784   | 0.008097166  | \n",
       "| 11089 | 9            | 0.192663323  | 0.186583917  | 0.215626585  | 0.196832282  | 0.223052452  | 0.1131780929 | 0.1949458484 | 0.172742001  | 0.20735334   | ⋯            | 0.159509202  | 0.15000000   | 0.190476190  | 0.08641975   | 0.20089286   | 0.212121212  | 0.195530726  | 0.2447917    | 0.22222222   | 0.214574899  | \n",
       "| 11090 | 9            | 0.023871397  | 0.032351776  | 0.028194535  | 0.021227655  | 0.029092994  | 0.0141797841 | 0.0286031658 | 0.019441069  | 0.02460124   | ⋯            | 0.030674847  | 0.03157895   | 0.011904762  | 0.01234568   | 0.02232143   | 0.026515152  | 0.005586592  | 0.0312500    | 0.02614379   | 0.032388664  | \n",
       "| 11091 | 9            | 0.124735602  | 0.061204278  | 0.090671885  | 0.122239748  | 0.112413997  | 0.0928840900 | 0.0824770897 | 0.130619684  | 0.11138145   | ⋯            | 0.073619632  | 0.01315789   | 0.113095238  | 0.02777778   | 0.10714286   | 0.071969697  | 0.089385475  | 0.0468750    | 0.09803922   | 0.028340081  | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "      target A           C           G           T           Total      \n",
       "11086 9      0.150843053 0.145450944 0.159237515 0.155757098 0.170932899\n",
       "11087 9      0.001329546 0.002376865 0.002536783 0.002168770 0.001886513\n",
       "11088 9      0.007554239 0.009045292 0.014350946 0.008017876 0.010320337\n",
       "11089 9      0.192663323 0.186583917 0.215626585 0.196832282 0.223052452\n",
       "11090 9      0.023871397 0.032351776 0.028194535 0.021227655 0.029092994\n",
       "11091 9      0.124735602 0.061204278 0.090671885 0.122239748 0.112413997\n",
       "      AA           AC           AT          AG         ⋯ GGCT        GGCG      \n",
       "11086 0.0947053467 0.1624548736 0.122114216 0.15788051 ⋯ 0.208588957 0.07368421\n",
       "11087 0.0006504488 0.0008331019 0.002430134 0.00162206 ⋯ 0.006134969 0.00000000\n",
       "11088 0.0031221543 0.0063871147 0.005872823 0.01432820 ⋯ 0.018404908 0.01842105\n",
       "11089 0.1131780929 0.1949458484 0.172742001 0.20735334 ⋯ 0.159509202 0.15000000\n",
       "11090 0.0141797841 0.0286031658 0.019441069 0.02460124 ⋯ 0.030674847 0.03157895\n",
       "11091 0.0928840900 0.0824770897 0.130619684 0.11138145 ⋯ 0.073619632 0.01315789\n",
       "      GGTA        GGTC       GGTT       GGTG        GGGA        GGGC     \n",
       "11086 0.154761905 0.09567901 0.11160714 0.200757576 0.167597765 0.1927083\n",
       "11087 0.000000000 0.00000000 0.00000000 0.003787879 0.000000000 0.0000000\n",
       "11088 0.005952381 0.00308642 0.01339286 0.007575758 0.027932961 0.0312500\n",
       "11089 0.190476190 0.08641975 0.20089286 0.212121212 0.195530726 0.2447917\n",
       "11090 0.011904762 0.01234568 0.02232143 0.026515152 0.005586592 0.0312500\n",
       "11091 0.113095238 0.02777778 0.10714286 0.071969697 0.089385475 0.0468750\n",
       "      GGGT       GGGG       \n",
       "11086 0.18300654 0.121457490\n",
       "11087 0.00000000 0.000000000\n",
       "11088 0.01960784 0.008097166\n",
       "11089 0.22222222 0.214574899\n",
       "11090 0.02614379 0.032388664\n",
       "11091 0.09803922 0.028340081"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Class 2, Subclass 1, Order TIR node features\n",
    "indx <- target[,1]==2 & !is.na(target[,4]) # Those in class 2 with known superfamily (All in Class 2 have subclass 1 and order TIR)\n",
    "tmp <- cbind(target[indx,4],data[indx,])\n",
    "names(tmp)[1] <- 'target'\n",
    "head(tmp)\n",
    "# res_class2 <- mRMR.ensemble(data = mRMR.data(tmp), solution_count=5, target_indices = 1, feature_count = 300, method='bootstrap')\n",
    "res_class2 <- mRMR.ensemble(data = mRMR.data(tmp), solution_count=1, target_indices = 1, feature_count = 300, method='exhaustive')\n",
    "rm(indx,tmp,target)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th scope=col>root</th><th scope=col>class1</th><th scope=col>class1OrderLTR</th><th scope=col>class1OrderLINE</th><th scope=col>class1OrderSINE</th><th scope=col>class2</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><td>288</td><td>145</td><td>265</td><td>128</td><td>294</td><td>237</td></tr>\n",
       "\t<tr><td>206</td><td>206</td><td>206</td><td>212</td><td>337</td><td>247</td></tr>\n",
       "\t<tr><td>247</td><td> 87</td><td> 87</td><td>339</td><td>157</td><td>206</td></tr>\n",
       "\t<tr><td>164</td><td>164</td><td>164</td><td>223</td><td>317</td><td>172</td></tr>\n",
       "\t<tr><td>269</td><td>189</td><td>189</td><td>171</td><td>178</td><td>223</td></tr>\n",
       "\t<tr><td>342</td><td>342</td><td>342</td><td>257</td><td>184</td><td> 94</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|llllll}\n",
       " root & class1 & class1OrderLTR & class1OrderLINE & class1OrderSINE & class2\\\\\n",
       "\\hline\n",
       "\t 288 & 145 & 265 & 128 & 294 & 237\\\\\n",
       "\t 206 & 206 & 206 & 212 & 337 & 247\\\\\n",
       "\t 247 &  87 &  87 & 339 & 157 & 206\\\\\n",
       "\t 164 & 164 & 164 & 223 & 317 & 172\\\\\n",
       "\t 269 & 189 & 189 & 171 & 178 & 223\\\\\n",
       "\t 342 & 342 & 342 & 257 & 184 &  94\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "root | class1 | class1OrderLTR | class1OrderLINE | class1OrderSINE | class2 | \n",
       "|---|---|---|---|---|---|\n",
       "| 288 | 145 | 265 | 128 | 294 | 237 | \n",
       "| 206 | 206 | 206 | 212 | 337 | 247 | \n",
       "| 247 |  87 |  87 | 339 | 157 | 206 | \n",
       "| 164 | 164 | 164 | 223 | 317 | 172 | \n",
       "| 269 | 189 | 189 | 171 | 178 | 223 | \n",
       "| 342 | 342 | 342 | 257 | 184 |  94 | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "  root class1 class1OrderLTR class1OrderLINE class1OrderSINE class2\n",
       "1 288  145    265            128             294             237   \n",
       "2 206  206    206            212             337             247   \n",
       "3 247   87     87            339             157             206   \n",
       "4 164  164    164            223             317             172   \n",
       "5 269  189    189            171             178             223   \n",
       "6 342  342    342            257             184              94   "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "res <- array(NA, dim=c(300,6))\n",
    "res[,1]=solutions(res_root)[[1]]\n",
    "res[,2]=solutions(res_class1)[[1]] \n",
    "res[,3]=solutions(res_class1orderLTR)[[1]] \n",
    "res[,4]=solutions(res_class1orderLINE)[[1]]\n",
    "res[,5]=solutions(res_class1orderSINE)[[1]]\n",
    "res[,6]=solutions(res_class2)[[1]]\n",
    "colnames(res) <- c('root','class1','class1OrderLTR', 'class1OrderLINE', 'class1OrderSINE', 'class2')\n",
    "res <- data.frame(res)\n",
    "head(res)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th scope=col>root</th><th scope=col>class1</th><th scope=col>class1OrderLTR</th><th scope=col>class1OrderLINE</th><th scope=col>class1OrderSINE</th><th scope=col>class2</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><td> 0.03605723 </td><td> 0.01390620 </td><td> 0.01160198 </td><td> 0.100516625</td><td>0.11503426  </td><td> 0.07555136 </td></tr>\n",
       "\t<tr><td>-0.13072318 </td><td>-0.03659201 </td><td>-0.01490437 </td><td>-0.002071081</td><td>0.04599622  </td><td>-0.16650545 </td></tr>\n",
       "\t<tr><td>-0.08572521 </td><td>-0.15233572 </td><td>-0.15065689 </td><td>-0.019113872</td><td>0.04676366  </td><td>-0.09566407 </td></tr>\n",
       "\t<tr><td>-0.18608936 </td><td>-0.15981561 </td><td>-0.14891868 </td><td>-0.014568071</td><td>0.02777371  </td><td>-0.13960142 </td></tr>\n",
       "\t<tr><td>-0.21565148 </td><td>-0.19951169 </td><td>-0.21261475 </td><td>-0.022920604</td><td>0.02443818  </td><td>-0.18131786 </td></tr>\n",
       "\t<tr><td>-0.21733296 </td><td>-0.21091751 </td><td>-0.21417004 </td><td>-0.007482423</td><td>0.01888730  </td><td>-0.18423519 </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|llllll}\n",
       " root & class1 & class1OrderLTR & class1OrderLINE & class1OrderSINE & class2\\\\\n",
       "\\hline\n",
       "\t  0.03605723  &  0.01390620  &  0.01160198  &  0.100516625 & 0.11503426   &  0.07555136 \\\\\n",
       "\t -0.13072318  & -0.03659201  & -0.01490437  & -0.002071081 & 0.04599622   & -0.16650545 \\\\\n",
       "\t -0.08572521  & -0.15233572  & -0.15065689  & -0.019113872 & 0.04676366   & -0.09566407 \\\\\n",
       "\t -0.18608936  & -0.15981561  & -0.14891868  & -0.014568071 & 0.02777371   & -0.13960142 \\\\\n",
       "\t -0.21565148  & -0.19951169  & -0.21261475  & -0.022920604 & 0.02443818   & -0.18131786 \\\\\n",
       "\t -0.21733296  & -0.21091751  & -0.21417004  & -0.007482423 & 0.01888730   & -0.18423519 \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "root | class1 | class1OrderLTR | class1OrderLINE | class1OrderSINE | class2 | \n",
       "|---|---|---|---|---|---|\n",
       "|  0.03605723  |  0.01390620  |  0.01160198  |  0.100516625 | 0.11503426   |  0.07555136  | \n",
       "| -0.13072318  | -0.03659201  | -0.01490437  | -0.002071081 | 0.04599622   | -0.16650545  | \n",
       "| -0.08572521  | -0.15233572  | -0.15065689  | -0.019113872 | 0.04676366   | -0.09566407  | \n",
       "| -0.18608936  | -0.15981561  | -0.14891868  | -0.014568071 | 0.02777371   | -0.13960142  | \n",
       "| -0.21565148  | -0.19951169  | -0.21261475  | -0.022920604 | 0.02443818   | -0.18131786  | \n",
       "| -0.21733296  | -0.21091751  | -0.21417004  | -0.007482423 | 0.01888730   | -0.18423519  | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "  root        class1      class1OrderLTR class1OrderLINE class1OrderSINE\n",
       "1  0.03605723  0.01390620  0.01160198     0.100516625    0.11503426     \n",
       "2 -0.13072318 -0.03659201 -0.01490437    -0.002071081    0.04599622     \n",
       "3 -0.08572521 -0.15233572 -0.15065689    -0.019113872    0.04676366     \n",
       "4 -0.18608936 -0.15981561 -0.14891868    -0.014568071    0.02777371     \n",
       "5 -0.21565148 -0.19951169 -0.21261475    -0.022920604    0.02443818     \n",
       "6 -0.21733296 -0.21091751 -0.21417004    -0.007482423    0.01888730     \n",
       "  class2     \n",
       "1  0.07555136\n",
       "2 -0.16650545\n",
       "3 -0.09566407\n",
       "4 -0.13960142\n",
       "5 -0.18131786\n",
       "6 -0.18423519"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "scor <- array(NA, dim=c(300,6))\n",
    "scor[,1]=scores(res_root)[[1]]\n",
    "scor[,2]=scores(res_class1)[[1]] \n",
    "scor[,3]=scores(res_class1orderLTR)[[1]] \n",
    "scor[,4]=scores(res_class1orderLINE)[[1]]\n",
    "scor[,5]=scores(res_class1orderSINE)[[1]]\n",
    "scor[,6]=scores(res_class2)[[1]]\n",
    "colnames(scor) <- c('root','class1','class1OrderLTR', 'class1OrderLINE', 'class1OrderSINE', 'class2')\n",
    "scor <- data.frame(scor)\n",
    "head(scor)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "write.table(res, file = \"mrmr_classic_features_norm.csv\",row.names=FALSE, na=\"\", col.names=TRUE, sep=\",\")\n",
    "write.table(scor, file = \"mrmr_classic_scores_norm.csv\",row.names=FALSE, na=\"\", col.names=TRUE, sep=\",\")"
   ]
  }
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