Bioactive_Molecular_Networks_v1.1_MZmine2.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Bioactive molecular networking notebook v1.1 (MZmine)\n",
    "\n",
    "Website: https://github.com/DorresteinLaboratory/Bioactive_Molecular_Networks\n",
    "\n",
    "The bioactive molecular network workflow integrates MS/MS molecular networking and bioassay-guided fractionation into the concept of bioactive molecular networking. The workflow relies on open bioinformatic tools, such MZmine2 [http://mzmine.github.io/] or Optimus (using OpenMS) [https://github.com/MolecularCartography/Optimus], a Jupyter notebook, and the GNPS web-platform (http://gnps.ucsd.edu). \n",
    "\n",
    "The code is released as a Jupyter notebook for easiness and reproducibility. The Jupyter notebook has been prepared by Dr. Ricardo Silva (UCSD).\n",
    "\n",
    "#### Citation: \n",
    "Bioactive molecular networking: Nothias, L.-F.; Nothias-Esposito, M.; da Silva, R.; Wang, M.; Protsyuk, I.; Zhang, Z.; Sarvepalli, A.; Leyssen, P.; Touboul, D.; Costa, J.; Paolini J., Alexandrov T., Litaudon M., Dorrestein, P. Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation. J. Nat. Prod. 2018. \n",
    "#### Manuscript: \n",
    "(Open access) https://pubs.acs.org/doi/10.1021/acs.jnatprod.7b00737\n",
    "\n",
    "### Instructions to run the notebook.\n",
    "\n",
    "-> This notebook is suitable for MZmine feature table.\n",
    "\n",
    "-> Make sure R is installed in your environment.\n",
    "\n",
    "-> Upload your files to the jupyter notebook folder.\n",
    "\n",
    "-> Update the filename if needed (in red) and indicated in the cell comments\n",
    "\n",
    "-> Run all cells by clicking on: Cell / Run All Below.\n",
    "\n",
    "-> Get the output file."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Lets run the bioactive molecular networking notebook !"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>588</li>\n",
       "\t<li>17</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 588\n",
       "\\item 17\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 588\n",
       "2. 17\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 588  17"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th scope=col>row ID</th><th scope=col>row m/z</th><th scope=col>row retention time</th><th scope=col>Extract.mzXML Peak area</th><th scope=col>F_5.mzXML Peak area</th><th scope=col>F_6.mzXML Peak area</th><th scope=col>F_7.mzXML Peak area</th><th scope=col>F_8.mzXML Peak area</th><th scope=col>F_9.mzXML Peak area</th><th scope=col>F_10.mzXML Peak area</th><th scope=col>F_11.mzXML Peak area</th><th scope=col>F_12.mzXML Peak area</th><th scope=col>F_13.mzXML Peak area</th><th scope=col>F_14.mzXML Peak area</th><th scope=col>F_15.mzXML Peak area</th><th scope=col>F_16.mzXML Peak area</th><th scope=col>F_17.mzXML Peak area</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><td>BioactivityCHIKV</td><td>     NA         </td><td>  NA            </td><td>     68.0       </td><td>        1       </td><td>        4.0     </td><td>        1.00    </td><td>        3.0     </td><td>       19.00    </td><td>       8        </td><td>       16       </td><td>       41.0     </td><td>     140.0      </td><td>      17.00     </td><td>      10.50     </td><td>       5        </td><td>      57        </td></tr>\n",
       "\t<tr><td>1               </td><td>270.279         </td><td>1698            </td><td>5690330.6       </td><td>246596026       </td><td>186949611.9     </td><td>362958584.30    </td><td>160968306.6     </td><td>100851795.00    </td><td>68548846        </td><td>141101389       </td><td>152605614.9     </td><td>50568985.2      </td><td>40253160.68     </td><td>51162993.45     </td><td>49859528        </td><td>49792597        </td></tr>\n",
       "\t<tr><td>2               </td><td>271.283         </td><td>1699            </td><td> 569378.1       </td><td> 40396490       </td><td> 30710029.2     </td><td> 63895441.00    </td><td> 26317669.9     </td><td> 16091012.72    </td><td>11523241        </td><td> 22836563       </td><td> 25351372.6     </td><td> 7873325.1      </td><td> 5872291.10     </td><td> 6356980.36     </td><td> 5143813        </td><td> 8061990        </td></tr>\n",
       "\t<tr><td>3               </td><td>279.174         </td><td>1413            </td><td>3172924.3       </td><td>        0       </td><td>        0.0     </td><td>        0.00    </td><td>        0.0     </td><td>    93954.37    </td><td>       0        </td><td>  1538466       </td><td> 62451927.9     </td><td>  410657.7      </td><td>   41184.01     </td><td>  118658.96     </td><td>       0        </td><td>       0        </td></tr>\n",
       "\t<tr><td>4               </td><td>280.264         </td><td>1420            </td><td>1821883.1       </td><td> 94393468       </td><td>   676012.6     </td><td>    97160.14    </td><td>   149605.1     </td><td>   199154.61    </td><td>       0        </td><td>        0       </td><td>   131789.8     </td><td> 2366320.9      </td><td>       0.00     </td><td>   25537.35     </td><td>13143595        </td><td> 2932929        </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|lllllllllllllllll}\n",
       " row ID & row m/z & row retention time & Extract.mzXML Peak area & F\\_5.mzXML Peak area & F\\_6.mzXML Peak area & F\\_7.mzXML Peak area & F\\_8.mzXML Peak area & F\\_9.mzXML Peak area & F\\_10.mzXML Peak area & F\\_11.mzXML Peak area & F\\_12.mzXML Peak area & F\\_13.mzXML Peak area & F\\_14.mzXML Peak area & F\\_15.mzXML Peak area & F\\_16.mzXML Peak area & F\\_17.mzXML Peak area\\\\\n",
       "\\hline\n",
       "\t BioactivityCHIKV &      NA          &   NA             &      68.0        &         1        &         4.0      &         1.00     &         3.0      &        19.00     &        8         &        16        &        41.0      &      140.0       &       17.00      &       10.50      &        5         &       57        \\\\\n",
       "\t 1                & 270.279          & 1698             & 5690330.6        & 246596026        & 186949611.9      & 362958584.30     & 160968306.6      & 100851795.00     & 68548846         & 141101389        & 152605614.9      & 50568985.2       & 40253160.68      & 51162993.45      & 49859528         & 49792597        \\\\\n",
       "\t 2                & 271.283          & 1699             &  569378.1        &  40396490        &  30710029.2      &  63895441.00     &  26317669.9      &  16091012.72     & 11523241         &  22836563        &  25351372.6      &  7873325.1       &  5872291.10      &  6356980.36      &  5143813         &  8061990        \\\\\n",
       "\t 3                & 279.174          & 1413             & 3172924.3        &         0        &         0.0      &         0.00     &         0.0      &     93954.37     &        0         &   1538466        &  62451927.9      &   410657.7       &    41184.01      &   118658.96      &        0         &        0        \\\\\n",
       "\t 4                & 280.264          & 1420             & 1821883.1        &  94393468        &    676012.6      &     97160.14     &    149605.1      &    199154.61     &        0         &         0        &    131789.8      &  2366320.9       &        0.00      &    25537.35      & 13143595         &  2932929        \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "row ID | row m/z | row retention time | Extract.mzXML Peak area | F_5.mzXML Peak area | F_6.mzXML Peak area | F_7.mzXML Peak area | F_8.mzXML Peak area | F_9.mzXML Peak area | F_10.mzXML Peak area | F_11.mzXML Peak area | F_12.mzXML Peak area | F_13.mzXML Peak area | F_14.mzXML Peak area | F_15.mzXML Peak area | F_16.mzXML Peak area | F_17.mzXML Peak area | \n",
       "|---|---|---|---|---|\n",
       "| BioactivityCHIKV |      NA          |   NA             |      68.0        |         1        |         4.0      |         1.00     |         3.0      |        19.00     |        8         |        16        |        41.0      |      140.0       |       17.00      |       10.50      |        5         |       57         | \n",
       "| 1                | 270.279          | 1698             | 5690330.6        | 246596026        | 186949611.9      | 362958584.30     | 160968306.6      | 100851795.00     | 68548846         | 141101389        | 152605614.9      | 50568985.2       | 40253160.68      | 51162993.45      | 49859528         | 49792597         | \n",
       "| 2                | 271.283          | 1699             |  569378.1        |  40396490        |  30710029.2      |  63895441.00     |  26317669.9      |  16091012.72     | 11523241         |  22836563        |  25351372.6      |  7873325.1       |  5872291.10      |  6356980.36      |  5143813         |  8061990         | \n",
       "| 3                | 279.174          | 1413             | 3172924.3        |         0        |         0.0      |         0.00     |         0.0      |     93954.37     |        0         |   1538466        |  62451927.9      |   410657.7       |    41184.01      |   118658.96      |        0         |        0         | \n",
       "| 4                | 280.264          | 1420             | 1821883.1        |  94393468        |    676012.6      |     97160.14     |    149605.1      |    199154.61     |        0         |         0        |    131789.8      |  2366320.9       |        0.00      |    25537.35      | 13143595         |  2932929         | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "  row ID           row m/z row retention time Extract.mzXML Peak area\n",
       "1 BioactivityCHIKV      NA   NA                    68.0              \n",
       "2 1                270.279 1698               5690330.6              \n",
       "3 2                271.283 1699                569378.1              \n",
       "4 3                279.174 1413               3172924.3              \n",
       "5 4                280.264 1420               1821883.1              \n",
       "  F_5.mzXML Peak area F_6.mzXML Peak area F_7.mzXML Peak area\n",
       "1         1                   4.0                 1.00       \n",
       "2 246596026           186949611.9         362958584.30       \n",
       "3  40396490            30710029.2          63895441.00       \n",
       "4         0                   0.0                 0.00       \n",
       "5  94393468              676012.6             97160.14       \n",
       "  F_8.mzXML Peak area F_9.mzXML Peak area F_10.mzXML Peak area\n",
       "1         3.0                19.00               8            \n",
       "2 160968306.6         100851795.00        68548846            \n",
       "3  26317669.9          16091012.72        11523241            \n",
       "4         0.0             93954.37               0            \n",
       "5    149605.1            199154.61               0            \n",
       "  F_11.mzXML Peak area F_12.mzXML Peak area F_13.mzXML Peak area\n",
       "1        16                   41.0               140.0          \n",
       "2 141101389            152605614.9          50568985.2          \n",
       "3  22836563             25351372.6           7873325.1          \n",
       "4   1538466             62451927.9            410657.7          \n",
       "5         0               131789.8           2366320.9          \n",
       "  F_14.mzXML Peak area F_15.mzXML Peak area F_16.mzXML Peak area\n",
       "1       17.00                10.50                 5            \n",
       "2 40253160.68          51162993.45          49859528            \n",
       "3  5872291.10           6356980.36           5143813            \n",
       "4    41184.01            118658.96                 0            \n",
       "5        0.00             25537.35          13143595            \n",
       "  F_17.mzXML Peak area\n",
       "1       57            \n",
       "2 49792597            \n",
       "3  8061990            \n",
       "4        0            \n",
       "5  2932929            "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Load and inspect the MZmine feature table with bioassay results\n",
    "# Change the name in the code below if needed (.CSV file in red)\n",
    "# NB: Make sure to add the value of bioactivity in the second row.\n",
    "in_tab <- read.csv(\"TEMPLATE_FILES//INPUT_FILE/features_quantification_matrix_edited_bioactivity_MZmine2.csv\", stringsAsFactor=FALSE, check.names=FALSE)\n",
    "dim(in_tab)\n",
    "in_tab[1:5,]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# Transpose and format column and row labels to follow the workflow below\n",
    "# Change the the 'BioactivityCHIKV' variable in red below to the column row index name \n",
    "# corresponding to the bioassay results\n",
    "tab <- t(in_tab[,-c(1:3)])\n",
    "tab <- data.frame(Sample_name=sub(\"\\\\.mzXML Peak area\", \"\", rownames(tab)), tab)\n",
    "colnames(tab)[-1] <- c('BioactivityCHIKV', apply(in_tab[,2:3][-1,], 1, paste, collapse='_'))\n",
    "rownames(tab) <- NULL"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th scope=col>Sample_name</th><th scope=col>BioactivityCHIKV</th><th scope=col>270.279_1698</th><th scope=col>271.283_1699</th><th scope=col>279.174_1413</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><td>Extract   </td><td>68        </td><td>  5690331 </td><td>  569378.1</td><td>3172924   </td></tr>\n",
       "\t<tr><td>F_5       </td><td> 1        </td><td>246596026 </td><td>40396489.5</td><td>      0   </td></tr>\n",
       "\t<tr><td>F_6       </td><td> 4        </td><td>186949612 </td><td>30710029.2</td><td>      0   </td></tr>\n",
       "\t<tr><td>F_7       </td><td> 1        </td><td>362958584 </td><td>63895441.0</td><td>      0   </td></tr>\n",
       "\t<tr><td>F_8       </td><td> 3        </td><td>160968307 </td><td>26317669.9</td><td>      0   </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|lllll}\n",
       " Sample\\_name & BioactivityCHIKV & 270.279\\_1698 & 271.283\\_1699 & 279.174\\_1413\\\\\n",
       "\\hline\n",
       "\t Extract    & 68         &   5690331  &   569378.1 & 3172924   \\\\\n",
       "\t F\\_5      &  1         & 246596026  & 40396489.5 &       0   \\\\\n",
       "\t F\\_6      &  4         & 186949612  & 30710029.2 &       0   \\\\\n",
       "\t F\\_7      &  1         & 362958584  & 63895441.0 &       0   \\\\\n",
       "\t F\\_8      &  3         & 160968307  & 26317669.9 &       0   \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "Sample_name | BioactivityCHIKV | 270.279_1698 | 271.283_1699 | 279.174_1413 | \n",
       "|---|---|---|---|---|\n",
       "| Extract    | 68         |   5690331  |   569378.1 | 3172924    | \n",
       "| F_5        |  1         | 246596026  | 40396489.5 |       0    | \n",
       "| F_6        |  4         | 186949612  | 30710029.2 |       0    | \n",
       "| F_7        |  1         | 362958584  | 63895441.0 |       0    | \n",
       "| F_8        |  3         | 160968307  | 26317669.9 |       0    | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "  Sample_name BioactivityCHIKV 270.279_1698 271.283_1699 279.174_1413\n",
       "1 Extract     68                 5690331      569378.1   3172924     \n",
       "2 F_5          1               246596026    40396489.5         0     \n",
       "3 F_6          4               186949612    30710029.2         0     \n",
       "4 F_7          1               362958584    63895441.0         0     \n",
       "5 F_8          3               160968307    26317669.9         0     "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Display the table \n",
    "tab[1:5,1:5]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# Take out blank rows in the table\n",
    "if(any(is.na(tab[,2]))) tab <- tab[!is.na(tab[,2]),]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# Add 1 to all to help scaling feature intensities and Normalize the features by TIC  \n",
    "# \n",
    "tab2 <- tab\n",
    "tab2[,-c(1:2)] <- t(apply(tab2[,-c(1:2)], 1, function(x) (x+1)/sum((x+1))))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<dl>\n",
       "\t<dt>$estimate</dt>\n",
       "\t\t<dd><strong>cor:</strong> -0.324377606725705</dd>\n",
       "\t<dt>$p.value</dt>\n",
       "\t\t<dd>0.257849356719369</dd>\n",
       "</dl>\n"
      ],
      "text/latex": [
       "\\begin{description}\n",
       "\\item[\\$estimate] \\textbf{cor:} -0.324377606725705\n",
       "\\item[\\$p.value] 0.257849356719369\n",
       "\\end{description}\n"
      ],
      "text/markdown": [
       "$estimate\n",
       ":   **cor:** -0.324377606725705\n",
       "$p.value\n",
       ":   0.257849356719369\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "$estimate\n",
       "       cor \n",
       "-0.3243776 \n",
       "\n",
       "$p.value\n",
       "[1] 0.2578494\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Calculate the correlation coefficient between a single feature and the bioactivity.\n",
    "# Scale should help correlation - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1534033/\n",
    "cor.test(scale(tab2[,2])[,1], scale(tab2[,3])[,1])[c(\"estimate\", \"p.value\")]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# How to do for all features\n",
    "ct <- t(sapply(3:ncol(tab2), function(x) unlist(cor.test(scale(tab2[,2])[,1], scale(tab2[,x])[,1])[c(\"estimate\", \"p.value\")])))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>14</li>\n",
       "\t<li>589</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 14\n",
       "\\item 589\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 14\n",
       "2. 589\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1]  14 589"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>587</li>\n",
       "\t<li>2</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 587\n",
       "\\item 2\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 587\n",
       "2. 2\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 587   2"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Show the dimensions of the features_quantificaton_matrix.csv\n",
    "dim(tab2)\n",
    "dim(ct)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th scope=col>Sample_name</th><th scope=col>BioactivityCHIKV</th><th scope=col>270.279_1698</th><th scope=col>271.283_1699</th><th scope=col>279.174_1413</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><td>cor               </td><td>0                 </td><td>-0.324377606725705</td><td>-0.318374649942669</td><td>0.11344978411662  </td></tr>\n",
       "\t<tr><td> p_value          </td><td>0                 </td><td>0.257849356719369 </td><td>0.267271199671765 </td><td>0.699375059832539 </td></tr>\n",
       "\t<tr><td>Extract           </td><td> 68.0             </td><td>0.0001391824      </td><td>0.0000139267      </td><td>7.760803e-05      </td></tr>\n",
       "\t<tr><td>F_5               </td><td>  1.0             </td><td>0.1594079650      </td><td>0.0261136500      </td><td>6.464336e-10      </td></tr>\n",
       "\t<tr><td>F_6               </td><td>  4.0             </td><td>0.0228397314      </td><td>0.0037518603      </td><td>1.221705e-10      </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{lllll}\n",
       " Sample\\_name & BioactivityCHIKV & 270.279\\_1698 & 271.283\\_1699 & 279.174\\_1413\\\\\n",
       "\\hline\n",
       "\t cor                & 0                  & -0.324377606725705 & -0.318374649942669 & 0.11344978411662  \\\\\n",
       "\t  p\\_value         & 0                  & 0.257849356719369  & 0.267271199671765  & 0.699375059832539 \\\\\n",
       "\t Extract            &  68.0              & 0.0001391824       & 0.0000139267       & 7.760803e-05      \\\\\n",
       "\t F\\_5              &   1.0              & 0.1594079650       & 0.0261136500       & 6.464336e-10      \\\\\n",
       "\t F\\_6              &   4.0              & 0.0228397314       & 0.0037518603       & 1.221705e-10      \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "Sample_name | BioactivityCHIKV | 270.279_1698 | 271.283_1699 | 279.174_1413 | \n",
       "|---|---|---|---|---|\n",
       "| cor                | 0                  | -0.324377606725705 | -0.318374649942669 | 0.11344978411662   | \n",
       "|  p_value           | 0                  | 0.257849356719369  | 0.267271199671765  | 0.699375059832539  | \n",
       "| Extract            |  68.0              | 0.0001391824       | 0.0000139267       | 7.760803e-05       | \n",
       "| F_5                |   1.0              | 0.1594079650       | 0.0261136500       | 6.464336e-10       | \n",
       "| F_6                |   4.0              | 0.0228397314       | 0.0037518603       | 1.221705e-10       | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "     Sample_name BioactivityCHIKV 270.279_1698       271.283_1699      \n",
       "[1,] cor         0                -0.324377606725705 -0.318374649942669\n",
       "[2,]  p_value    0                0.257849356719369  0.267271199671765 \n",
       "[3,] Extract      68.0            0.0001391824       0.0000139267      \n",
       "[4,] F_5           1.0            0.1594079650       0.0261136500      \n",
       "[5,] F_6           4.0            0.0228397314       0.0037518603      \n",
       "     279.174_1413     \n",
       "[1,] 0.11344978411662 \n",
       "[2,] 0.699375059832539\n",
       "[3,] 7.760803e-05     \n",
       "[4,] 6.464336e-10     \n",
       "[5,] 1.221705e-10     "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Create an output table with correlation coefficient value and p-value for every features\n",
    "\n",
    "ct <- rbind(c(\"cor\",\" p_value\"), c(0,0), ct)\n",
    "\n",
    "tab3 <- rbind(t(ct),  as.matrix(tab2))\n",
    "rownames(tab3) <- NULL\n",
    "tab3[1:5, 1:5]\n",
    "write.csv(tab3, \"features_quantification_matrix_edited_with_correlation.csv\", row.names=FALSE)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th scope=col>shared name</th><th scope=col>IDs</th><th scope=col>cor</th><th scope=col> p_value</th><th scope=col>Extract</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><td>                  </td><td>BioactivityCHIKV  </td><td>0                 </td><td>0                 </td><td> 68.0             </td></tr>\n",
       "\t<tr><td>1                 </td><td>270.279_1698      </td><td>-0.324377606725705</td><td>0.257849356719369 </td><td>0.0001391824      </td></tr>\n",
       "\t<tr><td>2                 </td><td>271.283_1699      </td><td>-0.318374649942669</td><td>0.267271199671765 </td><td>0.0000139267      </td></tr>\n",
       "\t<tr><td>3                 </td><td>279.174_1413      </td><td>0.11344978411662  </td><td>0.699375059832539 </td><td>7.760803e-05      </td></tr>\n",
       "\t<tr><td>4                 </td><td>280.264_1420      </td><td>-0.200702959079237</td><td>0.49145327312603  </td><td>4.456230e-05      </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{lllll}\n",
       " shared name & IDs & cor &  p\\_value & Extract\\\\\n",
       "\\hline\n",
       "\t                    & BioactivityCHIKV   & 0                  & 0                  &  68.0             \\\\\n",
       "\t 1                  & 270.279\\_1698     & -0.324377606725705 & 0.257849356719369  & 0.0001391824      \\\\\n",
       "\t 2                  & 271.283\\_1699     & -0.318374649942669 & 0.267271199671765  & 0.0000139267      \\\\\n",
       "\t 3                  & 279.174\\_1413     & 0.11344978411662   & 0.699375059832539  & 7.760803e-05      \\\\\n",
       "\t 4                  & 280.264\\_1420     & -0.200702959079237 & 0.49145327312603   & 4.456230e-05      \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "shared name | IDs | cor |  p_value | Extract | \n",
       "|---|---|---|---|---|\n",
       "|                    | BioactivityCHIKV   | 0                  | 0                  |  68.0              | \n",
       "| 1                  | 270.279_1698       | -0.324377606725705 | 0.257849356719369  | 0.0001391824       | \n",
       "| 2                  | 271.283_1699       | -0.318374649942669 | 0.267271199671765  | 0.0000139267       | \n",
       "| 3                  | 279.174_1413       | 0.11344978411662   | 0.699375059832539  | 7.760803e-05       | \n",
       "| 4                  | 280.264_1420       | -0.200702959079237 | 0.49145327312603   | 4.456230e-05       | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "     shared name IDs              cor                 p_value         \n",
       "[1,]             BioactivityCHIKV 0                  0                \n",
       "[2,] 1           270.279_1698     -0.324377606725705 0.257849356719369\n",
       "[3,] 2           271.283_1699     -0.318374649942669 0.267271199671765\n",
       "[4,] 3           279.174_1413     0.11344978411662   0.699375059832539\n",
       "[5,] 4           280.264_1420     -0.200702959079237 0.49145327312603 \n",
       "     Extract     \n",
       "[1,]  68.0       \n",
       "[2,] 0.0001391824\n",
       "[3,] 0.0000139267\n",
       "[4,] 7.760803e-05\n",
       "[5,] 4.456230e-05"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Tranpose the table for molecular networking mapping in Cytoscape\n",
    "new = t(tab3)\n",
    "colnames(new) = new[1,]\n",
    "new = new[-1,]\n",
    "new = cbind(0:(nrow(new)-1), rownames(new), new)\n",
    "rownames(new) <- NULL\n",
    "colnames(new)[1:2] <- c(\"shared name\", \"IDs\")\n",
    "new[1,1] <- \"\"\n",
    "new[1:5,1:5]\n",
    "write.csv(new, \"features_quantification_matrix_transposed_with_correlation.csv\", row.names=FALSE)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>17</li>\n",
       "\t<li>27</li>\n",
       "\t<li>29</li>\n",
       "\t<li>30</li>\n",
       "\t<li>94</li>\n",
       "\t<li>99</li>\n",
       "\t<li>100</li>\n",
       "\t<li>108</li>\n",
       "\t<li>115</li>\n",
       "\t<li>120</li>\n",
       "\t<li>137</li>\n",
       "\t<li>138</li>\n",
       "\t<li>157</li>\n",
       "\t<li>158</li>\n",
       "\t<li>162</li>\n",
       "\t<li>171</li>\n",
       "\t<li>183</li>\n",
       "\t<li>201</li>\n",
       "\t<li>202</li>\n",
       "\t<li>207</li>\n",
       "\t<li>210</li>\n",
       "\t<li>239</li>\n",
       "\t<li>241</li>\n",
       "\t<li>255</li>\n",
       "\t<li>285</li>\n",
       "\t<li>292</li>\n",
       "\t<li>299</li>\n",
       "\t<li>306</li>\n",
       "\t<li>323</li>\n",
       "\t<li>329</li>\n",
       "\t<li>331</li>\n",
       "\t<li>346</li>\n",
       "\t<li>357</li>\n",
       "\t<li>360</li>\n",
       "\t<li>366</li>\n",
       "\t<li>367</li>\n",
       "\t<li>370</li>\n",
       "\t<li>371</li>\n",
       "\t<li>390</li>\n",
       "\t<li>416</li>\n",
       "\t<li>431</li>\n",
       "\t<li>433</li>\n",
       "\t<li>440</li>\n",
       "\t<li>446</li>\n",
       "\t<li>461</li>\n",
       "\t<li>462</li>\n",
       "\t<li>467</li>\n",
       "\t<li>469</li>\n",
       "\t<li>476</li>\n",
       "\t<li>482</li>\n",
       "\t<li>487</li>\n",
       "\t<li>496</li>\n",
       "\t<li>504</li>\n",
       "\t<li>512</li>\n",
       "\t<li>513</li>\n",
       "\t<li>518</li>\n",
       "\t<li>524</li>\n",
       "\t<li>531</li>\n",
       "\t<li>543</li>\n",
       "\t<li>544</li>\n",
       "\t<li>545</li>\n",
       "\t<li>556</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 17\n",
       "\\item 27\n",
       "\\item 29\n",
       "\\item 30\n",
       "\\item 94\n",
       "\\item 99\n",
       "\\item 100\n",
       "\\item 108\n",
       "\\item 115\n",
       "\\item 120\n",
       "\\item 137\n",
       "\\item 138\n",
       "\\item 157\n",
       "\\item 158\n",
       "\\item 162\n",
       "\\item 171\n",
       "\\item 183\n",
       "\\item 201\n",
       "\\item 202\n",
       "\\item 207\n",
       "\\item 210\n",
       "\\item 239\n",
       "\\item 241\n",
       "\\item 255\n",
       "\\item 285\n",
       "\\item 292\n",
       "\\item 299\n",
       "\\item 306\n",
       "\\item 323\n",
       "\\item 329\n",
       "\\item 331\n",
       "\\item 346\n",
       "\\item 357\n",
       "\\item 360\n",
       "\\item 366\n",
       "\\item 367\n",
       "\\item 370\n",
       "\\item 371\n",
       "\\item 390\n",
       "\\item 416\n",
       "\\item 431\n",
       "\\item 433\n",
       "\\item 440\n",
       "\\item 446\n",
       "\\item 461\n",
       "\\item 462\n",
       "\\item 467\n",
       "\\item 469\n",
       "\\item 476\n",
       "\\item 482\n",
       "\\item 487\n",
       "\\item 496\n",
       "\\item 504\n",
       "\\item 512\n",
       "\\item 513\n",
       "\\item 518\n",
       "\\item 524\n",
       "\\item 531\n",
       "\\item 543\n",
       "\\item 544\n",
       "\\item 545\n",
       "\\item 556\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 17\n",
       "2. 27\n",
       "3. 29\n",
       "4. 30\n",
       "5. 94\n",
       "6. 99\n",
       "7. 100\n",
       "8. 108\n",
       "9. 115\n",
       "10. 120\n",
       "11. 137\n",
       "12. 138\n",
       "13. 157\n",
       "14. 158\n",
       "15. 162\n",
       "16. 171\n",
       "17. 183\n",
       "18. 201\n",
       "19. 202\n",
       "20. 207\n",
       "21. 210\n",
       "22. 239\n",
       "23. 241\n",
       "24. 255\n",
       "25. 285\n",
       "26. 292\n",
       "27. 299\n",
       "28. 306\n",
       "29. 323\n",
       "30. 329\n",
       "31. 331\n",
       "32. 346\n",
       "33. 357\n",
       "34. 360\n",
       "35. 366\n",
       "36. 367\n",
       "37. 370\n",
       "38. 371\n",
       "39. 390\n",
       "40. 416\n",
       "41. 431\n",
       "42. 433\n",
       "43. 440\n",
       "44. 446\n",
       "45. 461\n",
       "46. 462\n",
       "47. 467\n",
       "48. 469\n",
       "49. 476\n",
       "50. 482\n",
       "51. 487\n",
       "52. 496\n",
       "53. 504\n",
       "54. 512\n",
       "55. 513\n",
       "56. 518\n",
       "57. 524\n",
       "58. 531\n",
       "59. 543\n",
       "60. 544\n",
       "61. 545\n",
       "62. 556\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       " [1]  17  27  29  30  94  99 100 108 115 120 137 138 157 158 162 171 183 201 202\n",
       "[20] 207 210 239 241 255 285 292 299 306 323 329 331 346 357 360 366 367 370 371\n",
       "[39] 390 416 431 433 440 446 461 462 467 469 476 482 487 496 504 512 513 518 524\n",
       "[58] 531 543 544 545 556"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Get the significant correlation coefficients for both cases (>0.05)\n",
    "which(as.numeric(ct[-c(1,2),2])<0.05)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
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       "\t<li>'401.232_1527'</li>\n",
       "\t<li>'563.296_1291'</li>\n",
       "\t<li>'571.255_559'</li>\n",
       "\t<li>'571.301_1719'</li>\n",
       "\t<li>'577.265_998'</li>\n",
       "\t<li>'589.311_1520'</li>\n",
       "\t<li>'591.326_1626'</li>\n",
       "\t<li>'613.266_824'</li>\n",
       "\t<li>'613.266_874'</li>\n",
       "\t<li>'641.294_836'</li>\n",
       "\t<li>'641.294_742'</li>\n",
       "\t<li>'647.307_997'</li>\n",
       "\t<li>'661.287_945'</li>\n",
       "\t<li>'669.289_697'</li>\n",
       "\t<li>'681.29_558'</li>\n",
       "\t<li>'681.29_742'</li>\n",
       "\t<li>'683.303_823'</li>\n",
       "\t<li>'684.31_823'</li>\n",
       "\t<li>'701.314_827'</li>\n",
       "\t<li>'703.29_730'</li>\n",
       "\t<li>'709.284_697'</li>\n",
       "\t<li>'721.303_945'</li>\n",
       "\t<li>'723.299_822'</li>\n",
       "\t<li>'725.339_774'</li>\n",
       "\t<li>'730.34_898'</li>\n",
       "\t<li>'737.31_963'</li>\n",
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       "\t<li>'739.319_593'</li>\n",
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       "\t<li>'753.332_773'</li>\n",
       "\t<li>'757.285_870'</li>\n",
       "\t<li>'758.373_1047'</li>\n",
       "\t<li>'758.373_1257'</li>\n",
       "\t<li>'761.301_805'</li>\n",
       "\t<li>'761.301_595'</li>\n",
       "\t<li>'767.345_870'</li>\n",
       "\t<li>'780.353_1045'</li>\n",
       "\t<li>'789.332_870'</li>\n",
       "\t<li>'789.332_1014'</li>\n",
       "\t<li>'792.357_1201'</li>\n",
       "\t<li>'793.361_1211'</li>\n",
       "\t<li>'802.398_1055'</li>\n",
       "\t<li>'803.307_939'</li>\n",
       "\t<li>'806.335_1158'</li>\n",
       "\t<li>'806.335_1061'</li>\n",
       "\t<li>'814.337_1192'</li>\n",
       "\t<li>'817.321_1105'</li>\n",
       "\t<li>'820.349_1210'</li>\n",
       "\t<li>'824.377_1038'</li>\n",
       "\t<li>'828.318_1067'</li>\n",
       "\t<li>'834.368_1269'</li>\n",
       "\t<li>'834.368_1463'</li>\n",
       "\t<li>'836.384_1150'</li>\n",
       "\t<li>'840.319_1120'</li>\n",
       "\t<li>'844.411_1331'</li>\n",
       "\t<li>'856.348_1463'</li>\n",
       "\t<li>'856.348_1245'</li>\n",
       "\t<li>'858.369_1147'</li>\n",
       "\t<li>'866.393_1330'</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
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       "\\item '563.296\\_1291'\n",
       "\\item '571.255\\_559'\n",
       "\\item '571.301\\_1719'\n",
       "\\item '577.265\\_998'\n",
       "\\item '589.311\\_1520'\n",
       "\\item '591.326\\_1626'\n",
       "\\item '613.266\\_824'\n",
       "\\item '613.266\\_874'\n",
       "\\item '641.294\\_836'\n",
       "\\item '641.294\\_742'\n",
       "\\item '647.307\\_997'\n",
       "\\item '661.287\\_945'\n",
       "\\item '669.289\\_697'\n",
       "\\item '681.29\\_558'\n",
       "\\item '681.29\\_742'\n",
       "\\item '683.303\\_823'\n",
       "\\item '684.31\\_823'\n",
       "\\item '701.314\\_827'\n",
       "\\item '703.29\\_730'\n",
       "\\item '709.284\\_697'\n",
       "\\item '721.303\\_945'\n",
       "\\item '723.299\\_822'\n",
       "\\item '725.339\\_774'\n",
       "\\item '730.34\\_898'\n",
       "\\item '737.31\\_963'\n",
       "\\item '739.319\\_785'\n",
       "\\item '739.319\\_593'\n",
       "\\item '747.321\\_773'\n",
       "\\item '753.332\\_773'\n",
       "\\item '757.285\\_870'\n",
       "\\item '758.373\\_1047'\n",
       "\\item '758.373\\_1257'\n",
       "\\item '761.301\\_805'\n",
       "\\item '761.301\\_595'\n",
       "\\item '767.345\\_870'\n",
       "\\item '780.353\\_1045'\n",
       "\\item '789.332\\_870'\n",
       "\\item '789.332\\_1014'\n",
       "\\item '792.357\\_1201'\n",
       "\\item '793.361\\_1211'\n",
       "\\item '802.398\\_1055'\n",
       "\\item '803.307\\_939'\n",
       "\\item '806.335\\_1158'\n",
       "\\item '806.335\\_1061'\n",
       "\\item '814.337\\_1192'\n",
       "\\item '817.321\\_1105'\n",
       "\\item '820.349\\_1210'\n",
       "\\item '824.377\\_1038'\n",
       "\\item '828.318\\_1067'\n",
       "\\item '834.368\\_1269'\n",
       "\\item '834.368\\_1463'\n",
       "\\item '836.384\\_1150'\n",
       "\\item '840.319\\_1120'\n",
       "\\item '844.411\\_1331'\n",
       "\\item '856.348\\_1463'\n",
       "\\item '856.348\\_1245'\n",
       "\\item '858.369\\_1147'\n",
       "\\item '866.393\\_1330'\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. '383.222_1524'\n",
       "2. '401.232_1290'\n",
       "3. '401.232_1619'\n",
       "4. '401.232_1527'\n",
       "5. '563.296_1291'\n",
       "6. '571.255_559'\n",
       "7. '571.301_1719'\n",
       "8. '577.265_998'\n",
       "9. '589.311_1520'\n",
       "10. '591.326_1626'\n",
       "11. '613.266_824'\n",
       "12. '613.266_874'\n",
       "13. '641.294_836'\n",
       "14. '641.294_742'\n",
       "15. '647.307_997'\n",
       "16. '661.287_945'\n",
       "17. '669.289_697'\n",
       "18. '681.29_558'\n",
       "19. '681.29_742'\n",
       "20. '683.303_823'\n",
       "21. '684.31_823'\n",
       "22. '701.314_827'\n",
       "23. '703.29_730'\n",
       "24. '709.284_697'\n",
       "25. '721.303_945'\n",
       "26. '723.299_822'\n",
       "27. '725.339_774'\n",
       "28. '730.34_898'\n",
       "29. '737.31_963'\n",
       "30. '739.319_785'\n",
       "31. '739.319_593'\n",
       "32. '747.321_773'\n",
       "33. '753.332_773'\n",
       "34. '757.285_870'\n",
       "35. '758.373_1047'\n",
       "36. '758.373_1257'\n",
       "37. '761.301_805'\n",
       "38. '761.301_595'\n",
       "39. '767.345_870'\n",
       "40. '780.353_1045'\n",
       "41. '789.332_870'\n",
       "42. '789.332_1014'\n",
       "43. '792.357_1201'\n",
       "44. '793.361_1211'\n",
       "45. '802.398_1055'\n",
       "46. '803.307_939'\n",
       "47. '806.335_1158'\n",
       "48. '806.335_1061'\n",
       "49. '814.337_1192'\n",
       "50. '817.321_1105'\n",
       "51. '820.349_1210'\n",
       "52. '824.377_1038'\n",
       "53. '828.318_1067'\n",
       "54. '834.368_1269'\n",
       "55. '834.368_1463'\n",
       "56. '836.384_1150'\n",
       "57. '840.319_1120'\n",
       "58. '844.411_1331'\n",
       "59. '856.348_1463'\n",
       "60. '856.348_1245'\n",
       "61. '858.369_1147'\n",
       "62. '866.393_1330'\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       " [1] \"383.222_1524\" \"401.232_1290\" \"401.232_1619\" \"401.232_1527\" \"563.296_1291\"\n",
       " [6] \"571.255_559\"  \"571.301_1719\" \"577.265_998\"  \"589.311_1520\" \"591.326_1626\"\n",
       "[11] \"613.266_824\"  \"613.266_874\"  \"641.294_836\"  \"641.294_742\"  \"647.307_997\" \n",
       "[16] \"661.287_945\"  \"669.289_697\"  \"681.29_558\"   \"681.29_742\"   \"683.303_823\" \n",
       "[21] \"684.31_823\"   \"701.314_827\"  \"703.29_730\"   \"709.284_697\"  \"721.303_945\" \n",
       "[26] \"723.299_822\"  \"725.339_774\"  \"730.34_898\"   \"737.31_963\"   \"739.319_785\" \n",
       "[31] \"739.319_593\"  \"747.321_773\"  \"753.332_773\"  \"757.285_870\"  \"758.373_1047\"\n",
       "[36] \"758.373_1257\" \"761.301_805\"  \"761.301_595\"  \"767.345_870\"  \"780.353_1045\"\n",
       "[41] \"789.332_870\"  \"789.332_1014\" \"792.357_1201\" \"793.361_1211\" \"802.398_1055\"\n",
       "[46] \"803.307_939\"  \"806.335_1158\" \"806.335_1061\" \"814.337_1192\" \"817.321_1105\"\n",
       "[51] \"820.349_1210\" \"824.377_1038\" \"828.318_1067\" \"834.368_1269\" \"834.368_1463\"\n",
       "[56] \"836.384_1150\" \"840.319_1120\" \"844.411_1331\" \"856.348_1463\" \"856.348_1245\"\n",
       "[61] \"858.369_1147\" \"866.393_1330\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Show the features ID with correlation coefficient\n",
    "nm <- colnames(tab)\n",
    "nm[-c(1:2)][as.numeric(ct[-c(1,2),2])<0.05]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>27</li>\n",
       "\t<li>30</li>\n",
       "\t<li>94</li>\n",
       "\t<li>99</li>\n",
       "\t<li>108</li>\n",
       "\t<li>115</li>\n",
       "\t<li>120</li>\n",
       "\t<li>137</li>\n",
       "\t<li>138</li>\n",
       "\t<li>157</li>\n",
       "\t<li>162</li>\n",
       "\t<li>171</li>\n",
       "\t<li>183</li>\n",
       "\t<li>201</li>\n",
       "\t<li>207</li>\n",
       "\t<li>210</li>\n",
       "\t<li>239</li>\n",
       "\t<li>241</li>\n",
       "\t<li>255</li>\n",
       "\t<li>285</li>\n",
       "\t<li>299</li>\n",
       "\t<li>331</li>\n",
       "\t<li>346</li>\n",
       "\t<li>357</li>\n",
       "\t<li>360</li>\n",
       "\t<li>366</li>\n",
       "\t<li>367</li>\n",
       "\t<li>371</li>\n",
       "\t<li>390</li>\n",
       "\t<li>416</li>\n",
       "\t<li>431</li>\n",
       "\t<li>433</li>\n",
       "\t<li>446</li>\n",
       "\t<li>461</li>\n",
       "\t<li>462</li>\n",
       "\t<li>469</li>\n",
       "\t<li>487</li>\n",
       "\t<li>496</li>\n",
       "\t<li>504</li>\n",
       "\t<li>513</li>\n",
       "\t<li>518</li>\n",
       "\t<li>524</li>\n",
       "\t<li>543</li>\n",
       "\t<li>544</li>\n",
       "\t<li>545</li>\n",
       "\t<li>556</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 27\n",
       "\\item 30\n",
       "\\item 94\n",
       "\\item 99\n",
       "\\item 108\n",
       "\\item 115\n",
       "\\item 120\n",
       "\\item 137\n",
       "\\item 138\n",
       "\\item 157\n",
       "\\item 162\n",
       "\\item 171\n",
       "\\item 183\n",
       "\\item 201\n",
       "\\item 207\n",
       "\\item 210\n",
       "\\item 239\n",
       "\\item 241\n",
       "\\item 255\n",
       "\\item 285\n",
       "\\item 299\n",
       "\\item 331\n",
       "\\item 346\n",
       "\\item 357\n",
       "\\item 360\n",
       "\\item 366\n",
       "\\item 367\n",
       "\\item 371\n",
       "\\item 390\n",
       "\\item 416\n",
       "\\item 431\n",
       "\\item 433\n",
       "\\item 446\n",
       "\\item 461\n",
       "\\item 462\n",
       "\\item 469\n",
       "\\item 487\n",
       "\\item 496\n",
       "\\item 504\n",
       "\\item 513\n",
       "\\item 518\n",
       "\\item 524\n",
       "\\item 543\n",
       "\\item 544\n",
       "\\item 545\n",
       "\\item 556\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 27\n",
       "2. 30\n",
       "3. 94\n",
       "4. 99\n",
       "5. 108\n",
       "6. 115\n",
       "7. 120\n",
       "8. 137\n",
       "9. 138\n",
       "10. 157\n",
       "11. 162\n",
       "12. 171\n",
       "13. 183\n",
       "14. 201\n",
       "15. 207\n",
       "16. 210\n",
       "17. 239\n",
       "18. 241\n",
       "19. 255\n",
       "20. 285\n",
       "21. 299\n",
       "22. 331\n",
       "23. 346\n",
       "24. 357\n",
       "25. 360\n",
       "26. 366\n",
       "27. 367\n",
       "28. 371\n",
       "29. 390\n",
       "30. 416\n",
       "31. 431\n",
       "32. 433\n",
       "33. 446\n",
       "34. 461\n",
       "35. 462\n",
       "36. 469\n",
       "37. 487\n",
       "38. 496\n",
       "39. 504\n",
       "40. 513\n",
       "41. 518\n",
       "42. 524\n",
       "43. 543\n",
       "44. 544\n",
       "45. 545\n",
       "46. 556\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       " [1]  27  30  94  99 108 115 120 137 138 157 162 171 183 201 207 210 239 241 255\n",
       "[20] 285 299 331 346 357 360 366 367 371 390 416 431 433 446 461 462 469 487 496\n",
       "[39] 504 513 518 524 543 544 545 556"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Call the ID\n",
    "which(p.adjust(as.numeric(ct[-c(1:2),2]), method = \"bonferroni\")<0.05)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>'401.232_1290'</li>\n",
       "\t<li>'401.232_1527'</li>\n",
       "\t<li>'563.296_1291'</li>\n",
       "\t<li>'571.255_559'</li>\n",
       "\t<li>'577.265_998'</li>\n",
       "\t<li>'589.311_1520'</li>\n",
       "\t<li>'591.326_1626'</li>\n",
       "\t<li>'613.266_824'</li>\n",
       "\t<li>'613.266_874'</li>\n",
       "\t<li>'641.294_836'</li>\n",
       "\t<li>'647.307_997'</li>\n",
       "\t<li>'661.287_945'</li>\n",
       "\t<li>'669.289_697'</li>\n",
       "\t<li>'681.29_558'</li>\n",
       "\t<li>'683.303_823'</li>\n",
       "\t<li>'684.31_823'</li>\n",
       "\t<li>'701.314_827'</li>\n",
       "\t<li>'703.29_730'</li>\n",
       "\t<li>'709.284_697'</li>\n",
       "\t<li>'721.303_945'</li>\n",
       "\t<li>'725.339_774'</li>\n",
       "\t<li>'739.319_593'</li>\n",
       "\t<li>'747.321_773'</li>\n",
       "\t<li>'753.332_773'</li>\n",
       "\t<li>'757.285_870'</li>\n",
       "\t<li>'758.373_1047'</li>\n",
       "\t<li>'758.373_1257'</li>\n",
       "\t<li>'761.301_595'</li>\n",
       "\t<li>'767.345_870'</li>\n",
       "\t<li>'780.353_1045'</li>\n",
       "\t<li>'789.332_870'</li>\n",
       "\t<li>'789.332_1014'</li>\n",
       "\t<li>'793.361_1211'</li>\n",
       "\t<li>'802.398_1055'</li>\n",
       "\t<li>'803.307_939'</li>\n",
       "\t<li>'806.335_1061'</li>\n",
       "\t<li>'820.349_1210'</li>\n",
       "\t<li>'824.377_1038'</li>\n",
       "\t<li>'828.318_1067'</li>\n",
       "\t<li>'834.368_1463'</li>\n",
       "\t<li>'836.384_1150'</li>\n",
       "\t<li>'840.319_1120'</li>\n",
       "\t<li>'856.348_1463'</li>\n",
       "\t<li>'856.348_1245'</li>\n",
       "\t<li>'858.369_1147'</li>\n",
       "\t<li>'866.393_1330'</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item '401.232\\_1290'\n",
       "\\item '401.232\\_1527'\n",
       "\\item '563.296\\_1291'\n",
       "\\item '571.255\\_559'\n",
       "\\item '577.265\\_998'\n",
       "\\item '589.311\\_1520'\n",
       "\\item '591.326\\_1626'\n",
       "\\item '613.266\\_824'\n",
       "\\item '613.266\\_874'\n",
       "\\item '641.294\\_836'\n",
       "\\item '647.307\\_997'\n",
       "\\item '661.287\\_945'\n",
       "\\item '669.289\\_697'\n",
       "\\item '681.29\\_558'\n",
       "\\item '683.303\\_823'\n",
       "\\item '684.31\\_823'\n",
       "\\item '701.314\\_827'\n",
       "\\item '703.29\\_730'\n",
       "\\item '709.284\\_697'\n",
       "\\item '721.303\\_945'\n",
       "\\item '725.339\\_774'\n",
       "\\item '739.319\\_593'\n",
       "\\item '747.321\\_773'\n",
       "\\item '753.332\\_773'\n",
       "\\item '757.285\\_870'\n",
       "\\item '758.373\\_1047'\n",
       "\\item '758.373\\_1257'\n",
       "\\item '761.301\\_595'\n",
       "\\item '767.345\\_870'\n",
       "\\item '780.353\\_1045'\n",
       "\\item '789.332\\_870'\n",
       "\\item '789.332\\_1014'\n",
       "\\item '793.361\\_1211'\n",
       "\\item '802.398\\_1055'\n",
       "\\item '803.307\\_939'\n",
       "\\item '806.335\\_1061'\n",
       "\\item '820.349\\_1210'\n",
       "\\item '824.377\\_1038'\n",
       "\\item '828.318\\_1067'\n",
       "\\item '834.368\\_1463'\n",
       "\\item '836.384\\_1150'\n",
       "\\item '840.319\\_1120'\n",
       "\\item '856.348\\_1463'\n",
       "\\item '856.348\\_1245'\n",
       "\\item '858.369\\_1147'\n",
       "\\item '866.393\\_1330'\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. '401.232_1290'\n",
       "2. '401.232_1527'\n",
       "3. '563.296_1291'\n",
       "4. '571.255_559'\n",
       "5. '577.265_998'\n",
       "6. '589.311_1520'\n",
       "7. '591.326_1626'\n",
       "8. '613.266_824'\n",
       "9. '613.266_874'\n",
       "10. '641.294_836'\n",
       "11. '647.307_997'\n",
       "12. '661.287_945'\n",
       "13. '669.289_697'\n",
       "14. '681.29_558'\n",
       "15. '683.303_823'\n",
       "16. '684.31_823'\n",
       "17. '701.314_827'\n",
       "18. '703.29_730'\n",
       "19. '709.284_697'\n",
       "20. '721.303_945'\n",
       "21. '725.339_774'\n",
       "22. '739.319_593'\n",
       "23. '747.321_773'\n",
       "24. '753.332_773'\n",
       "25. '757.285_870'\n",
       "26. '758.373_1047'\n",
       "27. '758.373_1257'\n",
       "28. '761.301_595'\n",
       "29. '767.345_870'\n",
       "30. '780.353_1045'\n",
       "31. '789.332_870'\n",
       "32. '789.332_1014'\n",
       "33. '793.361_1211'\n",
       "34. '802.398_1055'\n",
       "35. '803.307_939'\n",
       "36. '806.335_1061'\n",
       "37. '820.349_1210'\n",
       "38. '824.377_1038'\n",
       "39. '828.318_1067'\n",
       "40. '834.368_1463'\n",
       "41. '836.384_1150'\n",
       "42. '840.319_1120'\n",
       "43. '856.348_1463'\n",
       "44. '856.348_1245'\n",
       "45. '858.369_1147'\n",
       "46. '866.393_1330'\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       " [1] \"401.232_1290\" \"401.232_1527\" \"563.296_1291\" \"571.255_559\"  \"577.265_998\" \n",
       " [6] \"589.311_1520\" \"591.326_1626\" \"613.266_824\"  \"613.266_874\"  \"641.294_836\" \n",
       "[11] \"647.307_997\"  \"661.287_945\"  \"669.289_697\"  \"681.29_558\"   \"683.303_823\" \n",
       "[16] \"684.31_823\"   \"701.314_827\"  \"703.29_730\"   \"709.284_697\"  \"721.303_945\" \n",
       "[21] \"725.339_774\"  \"739.319_593\"  \"747.321_773\"  \"753.332_773\"  \"757.285_870\" \n",
       "[26] \"758.373_1047\" \"758.373_1257\" \"761.301_595\"  \"767.345_870\"  \"780.353_1045\"\n",
       "[31] \"789.332_870\"  \"789.332_1014\" \"793.361_1211\" \"802.398_1055\" \"803.307_939\" \n",
       "[36] \"806.335_1061\" \"820.349_1210\" \"824.377_1038\" \"828.318_1067\" \"834.368_1463\"\n",
       "[41] \"836.384_1150\" \"840.319_1120\" \"856.348_1463\" \"856.348_1245\" \"858.369_1147\"\n",
       "[46] \"866.393_1330\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Features passing Bonferronii method\n",
    "nm[-c(1:2)][which(p.adjust(as.numeric(ct[-c(1:2),2]), method = \"bonferroni\")<0.05)]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th scope=col>shared name</th><th scope=col>IDs</th><th scope=col>cor</th><th scope=col> p_value</th><th scope=col>Extract</th><th scope=col>p_value_corrected</th><th scope=col>F_5</th><th scope=col>F_6</th><th scope=col>F_7</th><th scope=col>F_8</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><td>                   </td><td>BioactivityCHIKV   </td><td>0                  </td><td>0                  </td><td> 68.0              </td><td>0                  </td><td>  1.0              </td><td>  4.0              </td><td>  1.0              </td><td>  3.0              </td></tr>\n",
       "\t<tr><td>1                  </td><td>270.279_1698       </td><td>-0.324377606725705 </td><td>0.257849356719369  </td><td>0.0001391824       </td><td>1                  </td><td>0.1594079650       </td><td>0.0228397314       </td><td>0.3139762067       </td><td>0.0551088883       </td></tr>\n",
       "\t<tr><td>2                  </td><td>271.283_1699       </td><td>-0.318374649942669 </td><td>0.267271199671765  </td><td>0.0000139267       </td><td>1                  </td><td>0.0261136500       </td><td>0.0037518603       </td><td>0.0552725554       </td><td>0.0090100816       </td></tr>\n",
       "\t<tr><td>3                  </td><td>279.174_1413       </td><td>0.11344978411662   </td><td>0.699375059832539  </td><td>7.760803e-05       </td><td>1                  </td><td>6.464336e-10       </td><td>1.221705e-10       </td><td>8.650469e-10       </td><td>3.423586e-10       </td></tr>\n",
       "\t<tr><td>4                  </td><td>280.264_1420       </td><td>-0.200702959079237 </td><td>0.49145327312603   </td><td>4.456230e-05       </td><td>1                  </td><td>6.101911e-02       </td><td>8.258893e-05       </td><td>8.404894e-05       </td><td>5.121893e-05       </td></tr>\n",
       "\t<tr><td>5                  </td><td>281.19_1031        </td><td>-0.201330433729144 </td><td>0.490071225054009  </td><td>4.369353e-05       </td><td>1                  </td><td>6.464336e-10       </td><td>1.194904e-04       </td><td>2.992650e-02       </td><td>8.518229e-05       </td></tr>\n",
       "\t<tr><td>6                  </td><td>282.279_1660       </td><td>-0.201928970163321 </td><td>0.48875460960341   </td><td>4.563084e-04       </td><td>1                  </td><td>5.618968e-01       </td><td>1.014960e-03       </td><td>2.860098e-03       </td><td>9.171837e-04       </td></tr>\n",
       "\t<tr><td>7                  </td><td>297.185_1652       </td><td>-0.27121389090935  </td><td>0.348283666308653  </td><td>6.741464e-05       </td><td>1                  </td><td>6.464336e-10       </td><td>1.150745e-02       </td><td>8.201229e-03       </td><td>7.540400e-05       </td></tr>\n",
       "\t<tr><td>8                  </td><td>297.185_1556       </td><td>-0.214874888224598 </td><td>0.460688215436271  </td><td>3.286022e-04       </td><td>1                  </td><td>6.464336e-10       </td><td>4.233761e-03       </td><td>5.458206e-02       </td><td>4.329827e-04       </td></tr>\n",
       "\t<tr><td>9                  </td><td>298.311_1968       </td><td>-0.296642926666024 </td><td>0.3030698225754    </td><td>2.040302e-05       </td><td>1                  </td><td>2.699247e-02       </td><td>6.353464e-03       </td><td>7.801129e-02       </td><td>7.468284e-03       </td></tr>\n",
       "\t<tr><td>10                 </td><td>313.179_1721       </td><td>0.514149093415966  </td><td>0.0599876302308284 </td><td>8.948249e-04       </td><td>1                  </td><td>6.464336e-10       </td><td>2.849181e-04       </td><td>2.773147e-04       </td><td>1.615254e-05       </td></tr>\n",
       "\t<tr><td>11                 </td><td>315.195_1687       </td><td>-0.214387381474332 </td><td>0.461730687253729  </td><td>6.075624e-04       </td><td>1                  </td><td>6.464336e-10       </td><td>1.445606e-01       </td><td>2.564659e-02       </td><td>1.606978e-03       </td></tr>\n",
       "\t<tr><td>12                 </td><td>315.195_1777       </td><td>-0.20372853105752  </td><td>0.484806069511438  </td><td>9.569474e-05       </td><td>1                  </td><td>7.234580e-05       </td><td>2.708920e-02       </td><td>3.310437e-03       </td><td>1.601149e-04       </td></tr>\n",
       "\t<tr><td>13                 </td><td>341.267_1509       </td><td>-0.2053974044361   </td><td>0.481157749869592  </td><td>1.669249e-05       </td><td>1                  </td><td>6.464336e-10       </td><td>1.221705e-10       </td><td>1.456070e-03       </td><td>1.487605e-02       </td></tr>\n",
       "\t<tr><td>14                 </td><td>363.25_1511        </td><td>-0.207281369412495 </td><td>0.477054883790855  </td><td>8.686752e-06       </td><td>1                  </td><td>6.464336e-10       </td><td>1.221705e-10       </td><td>1.449499e-03       </td><td>1.355859e-02       </td></tr>\n",
       "\t<tr><td>15                 </td><td>383.165_564        </td><td>0.229673438354267  </td><td>0.42959512606125   </td><td>8.354078e-05       </td><td>1                  </td><td>6.464336e-10       </td><td>1.221705e-10       </td><td>8.650469e-10       </td><td>3.423586e-10       </td></tr>\n",
       "\t<tr><td>16                 </td><td>383.22_1668        </td><td>-0.187953232291067 </td><td>0.519922948532928  </td><td>4.680118e-04       </td><td>1                  </td><td>1.962724e-05       </td><td>3.305265e-06       </td><td>8.650469e-10       </td><td>1.703802e-02       </td></tr>\n",
       "\t<tr><td>17                 </td><td>383.222_1524       </td><td>0.534793863828435  </td><td>0.0487932731059066 </td><td>7.535002e-04       </td><td>1                  </td><td>6.464336e-10       </td><td>6.433913e-06       </td><td>8.650469e-10       </td><td>1.937745e-04       </td></tr>\n",
       "\t<tr><td>18                 </td><td>383.222_1615       </td><td>-0.037574232106698 </td><td>0.898524312804278  </td><td>3.551571e-03       </td><td>1                  </td><td>1.517113e-05       </td><td>6.781142e-06       </td><td>8.650469e-10       </td><td>3.491533e-03       </td></tr>\n",
       "\t<tr><td>19                 </td><td>383.222_1698       </td><td>-0.242985258089082 </td><td>0.402560883588054  </td><td>8.504989e-04       </td><td>1                  </td><td>6.464336e-10       </td><td>1.221705e-10       </td><td>1.978970e-03       </td><td>1.720463e-02       </td></tr>\n",
       "\t<tr><td>20                 </td><td>383.222_1407       </td><td>-0.0666029709839993</td><td>0.821029580534277  </td><td>1.763110e-03       </td><td>1                  </td><td>6.464336e-10       </td><td>1.221705e-10       </td><td>8.650469e-10       </td><td>6.174435e-04       </td></tr>\n",
       "\t<tr><td>21                 </td><td>387.216_1361       </td><td>0.281855815198855  </td><td>0.328930260816831  </td><td>2.230659e-04       </td><td>1                  </td><td>6.464336e-10       </td><td>1.221705e-10       </td><td>8.650469e-10       </td><td>3.423586e-10       </td></tr>\n",
       "\t<tr><td>22                 </td><td>393.166_642        </td><td>0.228387251366747  </td><td>0.432254605627892  </td><td>1.115320e-04       </td><td>1                  </td><td>6.464336e-10       </td><td>1.221705e-10       </td><td>8.650469e-10       </td><td>3.423586e-10       </td></tr>\n",
       "\t<tr><td>23                 </td><td>397.179_821        </td><td>0.211307326756097  </td><td>0.468343345973288  </td><td>1.363555e-05       </td><td>1                  </td><td>1.595529e-05       </td><td>1.221705e-10       </td><td>2.190143e-05       </td><td>3.423586e-10       </td></tr>\n",
       "\t<tr><td>24                 </td><td>397.18_672         </td><td>0.172207640811325  </td><td>0.556066648849158  </td><td>4.367197e-05       </td><td>1                  </td><td>6.464336e-10       </td><td>1.221705e-10       </td><td>8.650469e-10       </td><td>3.423586e-10       </td></tr>\n",
       "\t<tr><td>25                 </td><td>400.157_589        </td><td>0.228659476892485  </td><td>0.431691028838877  </td><td>3.814065e-05       </td><td>1                  </td><td>6.464336e-10       </td><td>1.221705e-10       </td><td>8.650469e-10       </td><td>3.423586e-10       </td></tr>\n",
       "\t<tr><td>26                 </td><td>400.175_809        </td><td>0.225954440307934  </td><td>0.43730753983575   </td><td>1.236224e-04       </td><td>1                  </td><td>6.464336e-10       </td><td>1.221705e-10       </td><td>8.650469e-10       </td><td>3.423586e-10       </td></tr>\n",
       "\t<tr><td>27                 </td><td>401.232_1290       </td><td>0.911533897243834  </td><td>5.7064270699847e-06</td><td>9.569529e-03       </td><td>0.00334967269008102</td><td>1.960109e-05       </td><td>2.601850e-05       </td><td>8.650469e-10       </td><td>5.627394e-05       </td></tr>\n",
       "\t<tr><td>28                 </td><td>401.232_1411       </td><td>0.156482370780623  </td><td>0.593185890419915  </td><td>1.867191e-03       </td><td>1                  </td><td>6.464336e-10       </td><td>1.221705e-10       </td><td>8.650469e-10       </td><td>3.423586e-10       </td></tr>\n",
       "\t<tr><td>29                 </td><td>401.232_1619       </td><td>0.640073772749594  </td><td>0.0136797352409133 </td><td>1.046219e-02       </td><td>1                  </td><td>6.464336e-10       </td><td>1.221705e-10       </td><td>8.650469e-10       </td><td>4.234155e-05       </td></tr>\n",
       "\t<tr><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td></tr>\n",
       "\t<tr><td>558                 </td><td>868.356_1418        </td><td>-0.123916349672485  </td><td>0.67298286230042    </td><td>2.423684e-04        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>559                 </td><td>869.352_941         </td><td>0.228871589198768   </td><td>0.431252158342323   </td><td>5.189897e-03        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>560                 </td><td>869.392_1670        </td><td>-0.138127625586833  </td><td>0.637705709112937   </td><td>1.943030e-04        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>561                 </td><td>870.361_1433        </td><td>-0.142327465996463  </td><td>0.627411366909868   </td><td>2.407108e-05        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>562                 </td><td>872.373_933         </td><td>-0.169581520797562  </td><td>0.562196424949146   </td><td>6.360730e-06        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>563                 </td><td>872.373_867         </td><td>-0.17168074681055   </td><td>0.557294227073848   </td><td>2.448277e-05        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>564                 </td><td>874.363_1337        </td><td>-0.0762150612440404 </td><td>0.79566697946497    </td><td>4.025099e-05        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>565                 </td><td>881.32_878          </td><td>-0.0456016842842233 </td><td>0.876981592762568   </td><td>4.137304e-04        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>566                 </td><td>882.33_1231         </td><td>0.215278406255525   </td><td>0.459826208385533   </td><td>3.714671e-04        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>567                 </td><td>883.33_776          </td><td>0.22762293857456    </td><td>0.43383890536112    </td><td>1.134265e-03        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>568                 </td><td>883.36_1084         </td><td>0.226857086624798   </td><td>0.435429313884083   </td><td>1.049822e-03        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>569                 </td><td>884.403_1197        </td><td>-0.19571665652726   </td><td>0.502500080797765   </td><td>3.416119e-05        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>570                 </td><td>885.328_1499        </td><td>-0.140168489162022  </td><td>0.632695569993799   </td><td>7.163746e-04        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>571                 </td><td>890.336_1433        </td><td>-0.173610421967432  </td><td>0.552803995293411   </td><td>7.736488e-05        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>572                 </td><td>890.376_857         </td><td>-0.170642781563919  </td><td>0.559715865190782   </td><td>2.445946e-11        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>573                 </td><td>891.33_941          </td><td>0.235112721192342   </td><td>0.418440050952477   </td><td>2.963642e-04        </td><td>1                   </td><td>1.903514e-05        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>574                 </td><td>892.407_1610        </td><td>-0.0367844701475624 </td><td>0.900647487143874   </td><td>2.354112e-04        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>575                 </td><td>893.416_1609        </td><td>-0.0400530918407881 </td><td>0.891864372574871   </td><td>1.180280e-04        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>576                 </td><td>894.426_1631        </td><td>0.00495069939264375 </td><td>0.986598849465163   </td><td>8.715378e-05        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>577                 </td><td>895.374_1424        </td><td>-0.0610903099469755 </td><td>0.835650657086433   </td><td>5.474881e-05        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>578                 </td><td>895.407_1768        </td><td>-0.0979804586462028 </td><td>0.738959134381491   </td><td>6.713617e-04        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>579                 </td><td>897.375_1333        </td><td>0.219605705905163   </td><td>0.450631623694371   </td><td>2.554670e-05        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>580                 </td><td>903.335_1024        </td><td>0.229358628939693   </td><td>0.430245300634323   </td><td>7.472515e-04        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>581                 </td><td>905.349_1085        </td><td>0.242771404102679   </td><td>0.40298803522669    </td><td>2.531490e-04        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>582                 </td><td>906.39_1200         </td><td>-0.197018302170316  </td><td>0.499605428975835   </td><td>4.226406e-05        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>583                 </td><td>914.392_1610        </td><td>-0.00750358060402209</td><td>0.97968947879799    </td><td>2.373081e-04        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>584                 </td><td>916.412_1631        </td><td>0.0473109703903092  </td><td>0.872404223005271   </td><td>6.811799e-05        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>585                 </td><td>927.391_1213        </td><td>-0.171019340513868  </td><td>0.558836817323772   </td><td>2.445946e-11        </td><td>1                   </td><td>6.464336e-10        </td><td>1.221705e-10        </td><td>8.650469e-10        </td><td>3.423586e-10        </td></tr>\n",
       "\t<tr><td>586                 </td><td>983.559_1688        </td><td>-0.185422040102229  </td><td>0.525661291436393   </td><td>5.060243e-04        </td><td>1                   </td><td>1.412577e-04        </td><td>2.424826e-01        </td><td>8.936452e-03        </td><td>6.439997e-05        </td></tr>\n",
       "\t<tr><td>587                 </td><td>987.593_1777        </td><td>-0.179208062169923  </td><td>0.539866703843945   </td><td>1.229554e-05        </td><td>1                   </td><td>6.464336e-10        </td><td>4.639795e-02        </td><td>2.693216e-04        </td><td>3.423586e-10        </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{llllllllll}\n",
       " shared name & IDs & cor &  p\\_value & Extract & p\\_value\\_corrected & F\\_5 & F\\_6 & F\\_7 & F\\_8\\\\\n",
       "\\hline\n",
       "\t                     & BioactivityCHIKV    & 0                   & 0                   &  68.0               & 0                   &   1.0               &   4.0               &   1.0               &   3.0              \\\\\n",
       "\t 1                   & 270.279\\_1698      & -0.324377606725705  & 0.257849356719369   & 0.0001391824        & 1                   & 0.1594079650        & 0.0228397314        & 0.3139762067        & 0.0551088883       \\\\\n",
       "\t 2                   & 271.283\\_1699      & -0.318374649942669  & 0.267271199671765   & 0.0000139267        & 1                   & 0.0261136500        & 0.0037518603        & 0.0552725554        & 0.0090100816       \\\\\n",
       "\t 3                   & 279.174\\_1413      & 0.11344978411662    & 0.699375059832539   & 7.760803e-05        & 1                   & 6.464336e-10        & 1.221705e-10        & 8.650469e-10        & 3.423586e-10       \\\\\n",
       "\t 4                   & 280.264\\_1420      & -0.200702959079237  & 0.49145327312603    & 4.456230e-05        & 1                   & 6.101911e-02        & 8.258893e-05        & 8.404894e-05        & 5.121893e-05       \\\\\n",
       "\t 5                   & 281.19\\_1031       & -0.201330433729144  & 0.490071225054009   & 4.369353e-05        & 1                   & 6.464336e-10        & 1.194904e-04        & 2.992650e-02        & 8.518229e-05       \\\\\n",
       "\t 6                   & 282.279\\_1660      & -0.201928970163321  & 0.48875460960341    & 4.563084e-04        & 1                   & 5.618968e-01        & 1.014960e-03        & 2.860098e-03        & 9.171837e-04       \\\\\n",
       "\t 7                   & 297.185\\_1652      & -0.27121389090935   & 0.348283666308653   & 6.741464e-05        & 1                   & 6.464336e-10        & 1.150745e-02        & 8.201229e-03        & 7.540400e-05       \\\\\n",
       "\t 8                   & 297.185\\_1556      & -0.214874888224598  & 0.460688215436271   & 3.286022e-04        & 1                   & 6.464336e-10        & 4.233761e-03        & 5.458206e-02        & 4.329827e-04       \\\\\n",
       "\t 9                   & 298.311\\_1968      & -0.296642926666024  & 0.3030698225754     & 2.040302e-05        & 1                   & 2.699247e-02        & 6.353464e-03        & 7.801129e-02        & 7.468284e-03       \\\\\n",
       "\t 10                  & 313.179\\_1721      & 0.514149093415966   & 0.0599876302308284  & 8.948249e-04        & 1                   & 6.464336e-10        & 2.849181e-04        & 2.773147e-04        & 1.615254e-05       \\\\\n",
       "\t 11                  & 315.195\\_1687      & -0.214387381474332  & 0.461730687253729   & 6.075624e-04        & 1                   & 6.464336e-10        & 1.445606e-01        & 2.564659e-02        & 1.606978e-03       \\\\\n",
       "\t 12                  & 315.195\\_1777      & -0.20372853105752   & 0.484806069511438   & 9.569474e-05        & 1                   & 7.234580e-05        & 2.708920e-02        & 3.310437e-03        & 1.601149e-04       \\\\\n",
       "\t 13                  & 341.267\\_1509      & -0.2053974044361    & 0.481157749869592   & 1.669249e-05        & 1                   & 6.464336e-10        & 1.221705e-10        & 1.456070e-03        & 1.487605e-02       \\\\\n",
       "\t 14                  & 363.25\\_1511       & -0.207281369412495  & 0.477054883790855   & 8.686752e-06        & 1                   & 6.464336e-10        & 1.221705e-10        & 1.449499e-03        & 1.355859e-02       \\\\\n",
       "\t 15                  & 383.165\\_564       & 0.229673438354267   & 0.42959512606125    & 8.354078e-05        & 1                   & 6.464336e-10        & 1.221705e-10        & 8.650469e-10        & 3.423586e-10       \\\\\n",
       "\t 16                  & 383.22\\_1668       & -0.187953232291067  & 0.519922948532928   & 4.680118e-04        & 1                   & 1.962724e-05        & 3.305265e-06        & 8.650469e-10        & 1.703802e-02       \\\\\n",
       "\t 17                  & 383.222\\_1524      & 0.534793863828435   & 0.0487932731059066  & 7.535002e-04        & 1                   & 6.464336e-10        & 6.433913e-06        & 8.650469e-10        & 1.937745e-04       \\\\\n",
       "\t 18                  & 383.222\\_1615      & -0.037574232106698  & 0.898524312804278   & 3.551571e-03        & 1                   & 1.517113e-05        & 6.781142e-06        & 8.650469e-10        & 3.491533e-03       \\\\\n",
       "\t 19                  & 383.222\\_1698      & -0.242985258089082  & 0.402560883588054   & 8.504989e-04        & 1                   & 6.464336e-10        & 1.221705e-10        & 1.978970e-03        & 1.720463e-02       \\\\\n",
       "\t 20                  & 383.222\\_1407      & -0.0666029709839993 & 0.821029580534277   & 1.763110e-03        & 1                   & 6.464336e-10        & 1.221705e-10        & 8.650469e-10        & 6.174435e-04       \\\\\n",
       "\t 21                  & 387.216\\_1361      & 0.281855815198855   & 0.328930260816831   & 2.230659e-04        & 1                   & 6.464336e-10        & 1.221705e-10        & 8.650469e-10        & 3.423586e-10       \\\\\n",
       "\t 22                  & 393.166\\_642       & 0.228387251366747   & 0.432254605627892   & 1.115320e-04        & 1                   & 6.464336e-10        & 1.221705e-10        & 8.650469e-10        & 3.423586e-10       \\\\\n",
       "\t 23                  & 397.179\\_821       & 0.211307326756097   & 0.468343345973288   & 1.363555e-05        & 1                   & 1.595529e-05        & 1.221705e-10        & 2.190143e-05        & 3.423586e-10       \\\\\n",
       "\t 24                  & 397.18\\_672        & 0.172207640811325   & 0.556066648849158   & 4.367197e-05        & 1                   & 6.464336e-10        & 1.221705e-10        & 8.650469e-10        & 3.423586e-10       \\\\\n",
       "\t 25                  & 400.157\\_589       & 0.228659476892485   & 0.431691028838877   & 3.814065e-05        & 1                   & 6.464336e-10        & 1.221705e-10        & 8.650469e-10        & 3.423586e-10       \\\\\n",
       "\t 26                  & 400.175\\_809       & 0.225954440307934   & 0.43730753983575    & 1.236224e-04        & 1                   & 6.464336e-10        & 1.221705e-10        & 8.650469e-10        & 3.423586e-10       \\\\\n",
       "\t 27                  & 401.232\\_1290      & 0.911533897243834   & 5.7064270699847e-06 & 9.569529e-03        & 0.00334967269008102 & 1.960109e-05        & 2.601850e-05        & 8.650469e-10        & 5.627394e-05       \\\\\n",
       "\t 28                  & 401.232\\_1411      & 0.156482370780623   & 0.593185890419915   & 1.867191e-03        & 1                   & 6.464336e-10        & 1.221705e-10        & 8.650469e-10        & 3.423586e-10       \\\\\n",
       "\t 29                  & 401.232\\_1619      & 0.640073772749594   & 0.0136797352409133  & 1.046219e-02        & 1                   & 6.464336e-10        & 1.221705e-10        & 8.650469e-10        & 4.234155e-05       \\\\\n",
       "\t ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮\\\\\n",
       "\t 558                  & 868.356\\_1418       & -0.123916349672485   & 0.67298286230042     & 2.423684e-04         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 559                  & 869.352\\_941        & 0.228871589198768    & 0.431252158342323    & 5.189897e-03         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 560                  & 869.392\\_1670       & -0.138127625586833   & 0.637705709112937    & 1.943030e-04         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 561                  & 870.361\\_1433       & -0.142327465996463   & 0.627411366909868    & 2.407108e-05         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 562                  & 872.373\\_933        & -0.169581520797562   & 0.562196424949146    & 6.360730e-06         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 563                  & 872.373\\_867        & -0.17168074681055    & 0.557294227073848    & 2.448277e-05         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 564                  & 874.363\\_1337       & -0.0762150612440404  & 0.79566697946497     & 4.025099e-05         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 565                  & 881.32\\_878         & -0.0456016842842233  & 0.876981592762568    & 4.137304e-04         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 566                  & 882.33\\_1231        & 0.215278406255525    & 0.459826208385533    & 3.714671e-04         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 567                  & 883.33\\_776         & 0.22762293857456     & 0.43383890536112     & 1.134265e-03         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 568                  & 883.36\\_1084        & 0.226857086624798    & 0.435429313884083    & 1.049822e-03         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 569                  & 884.403\\_1197       & -0.19571665652726    & 0.502500080797765    & 3.416119e-05         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 570                  & 885.328\\_1499       & -0.140168489162022   & 0.632695569993799    & 7.163746e-04         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 571                  & 890.336\\_1433       & -0.173610421967432   & 0.552803995293411    & 7.736488e-05         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 572                  & 890.376\\_857        & -0.170642781563919   & 0.559715865190782    & 2.445946e-11         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 573                  & 891.33\\_941         & 0.235112721192342    & 0.418440050952477    & 2.963642e-04         & 1                    & 1.903514e-05         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 574                  & 892.407\\_1610       & -0.0367844701475624  & 0.900647487143874    & 2.354112e-04         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 575                  & 893.416\\_1609       & -0.0400530918407881  & 0.891864372574871    & 1.180280e-04         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 576                  & 894.426\\_1631       & 0.00495069939264375  & 0.986598849465163    & 8.715378e-05         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 577                  & 895.374\\_1424       & -0.0610903099469755  & 0.835650657086433    & 5.474881e-05         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 578                  & 895.407\\_1768       & -0.0979804586462028  & 0.738959134381491    & 6.713617e-04         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 579                  & 897.375\\_1333       & 0.219605705905163    & 0.450631623694371    & 2.554670e-05         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 580                  & 903.335\\_1024       & 0.229358628939693    & 0.430245300634323    & 7.472515e-04         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 581                  & 905.349\\_1085       & 0.242771404102679    & 0.40298803522669     & 2.531490e-04         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 582                  & 906.39\\_1200        & -0.197018302170316   & 0.499605428975835    & 4.226406e-05         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 583                  & 914.392\\_1610       & -0.00750358060402209 & 0.97968947879799     & 2.373081e-04         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 584                  & 916.412\\_1631       & 0.0473109703903092   & 0.872404223005271    & 6.811799e-05         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 585                  & 927.391\\_1213       & -0.171019340513868   & 0.558836817323772    & 2.445946e-11         & 1                    & 6.464336e-10         & 1.221705e-10         & 8.650469e-10         & 3.423586e-10        \\\\\n",
       "\t 586                  & 983.559\\_1688       & -0.185422040102229   & 0.525661291436393    & 5.060243e-04         & 1                    & 1.412577e-04         & 2.424826e-01         & 8.936452e-03         & 6.439997e-05        \\\\\n",
       "\t 587                  & 987.593\\_1777       & -0.179208062169923   & 0.539866703843945    & 1.229554e-05         & 1                    & 6.464336e-10         & 4.639795e-02         & 2.693216e-04         & 3.423586e-10        \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "shared name | IDs | cor |  p_value | Extract | p_value_corrected | F_5 | F_6 | F_7 | F_8 | \n",
       "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
       "|                     | BioactivityCHIKV    | 0                   | 0                   |  68.0               | 0                   |   1.0               |   4.0               |   1.0               |   3.0               | \n",
       "| 1                   | 270.279_1698        | -0.324377606725705  | 0.257849356719369   | 0.0001391824        | 1                   | 0.1594079650        | 0.0228397314        | 0.3139762067        | 0.0551088883        | \n",
       "| 2                   | 271.283_1699        | -0.318374649942669  | 0.267271199671765   | 0.0000139267        | 1                   | 0.0261136500        | 0.0037518603        | 0.0552725554        | 0.0090100816        | \n",
       "| 3                   | 279.174_1413        | 0.11344978411662    | 0.699375059832539   | 7.760803e-05        | 1                   | 6.464336e-10        | 1.221705e-10        | 8.650469e-10        | 3.423586e-10        | \n",
       "| 4                   | 280.264_1420        | -0.200702959079237  | 0.49145327312603    | 4.456230e-05        | 1                   | 6.101911e-02        | 8.258893e-05        | 8.404894e-05        | 5.121893e-05        | \n",
       "| 5                   | 281.19_1031         | -0.201330433729144  | 0.490071225054009   | 4.369353e-05        | 1                   | 6.464336e-10        | 1.194904e-04        | 2.992650e-02        | 8.518229e-05        | \n",
       "| 6                   | 282.279_1660        | -0.201928970163321  | 0.48875460960341    | 4.563084e-04        | 1                   | 5.618968e-01        | 1.014960e-03        | 2.860098e-03        | 9.171837e-04        | \n",
       "| 7                   | 297.185_1652        | -0.27121389090935   | 0.348283666308653   | 6.741464e-05        | 1                   | 6.464336e-10        | 1.150745e-02        | 8.201229e-03        | 7.540400e-05        | \n",
       "| 8                   | 297.185_1556        | -0.214874888224598  | 0.460688215436271   | 3.286022e-04        | 1                   | 6.464336e-10        | 4.233761e-03        | 5.458206e-02        | 4.329827e-04        | \n",
       "| 9                   | 298.311_1968        | -0.296642926666024  | 0.3030698225754     | 2.040302e-05        | 1                   | 2.699247e-02        | 6.353464e-03        | 7.801129e-02        | 7.468284e-03        | \n",
       "| 10                  | 313.179_1721        | 0.514149093415966   | 0.0599876302308284  | 8.948249e-04        | 1                   | 6.464336e-10        | 2.849181e-04        | 2.773147e-04        | 1.615254e-05        | \n",
       "| 11                  | 315.195_1687        | -0.214387381474332  | 0.461730687253729   | 6.075624e-04        | 1                   | 6.464336e-10        | 1.445606e-01        | 2.564659e-02        | 1.606978e-03        | \n",
       "| 12                  | 315.195_1777        | -0.20372853105752   | 0.484806069511438   | 9.569474e-05        | 1                   | 7.234580e-05        | 2.708920e-02        | 3.310437e-03        | 1.601149e-04        | \n",
       "| 13                  | 341.267_1509        | -0.2053974044361    | 0.481157749869592   | 1.669249e-05        | 1                   | 6.464336e-10        | 1.221705e-10        | 1.456070e-03        | 1.487605e-02        | \n",
       "| 14                  | 363.25_1511         | -0.207281369412495  | 0.477054883790855   | 8.686752e-06        | 1                   | 6.464336e-10        | 1.221705e-10        | 1.449499e-03        | 1.355859e-02        | \n",
       "| 15                  | 383.165_564         | 0.229673438354267   | 0.42959512606125    | 8.354078e-05        | 1                   | 6.464336e-10        | 1.221705e-10        | 8.650469e-10        | 3.423586e-10        | \n",
       "| 16                  | 383.22_1668         | -0.187953232291067  | 0.519922948532928   | 4.680118e-04        | 1                   | 1.962724e-05        | 3.305265e-06        | 8.650469e-10        | 1.703802e-02        | \n",
       "| 17                  | 383.222_1524        | 0.534793863828435   | 0.0487932731059066  | 7.535002e-04        | 1                   | 6.464336e-10        | 6.433913e-06        | 8.650469e-10        | 1.937745e-04        | \n",
       "| 18                  | 383.222_1615        | -0.037574232106698  | 0.898524312804278   | 3.551571e-03        | 1                   | 1.517113e-05        | 6.781142e-06        | 8.650469e-10        | 3.491533e-03        | \n",
       "| 19                  | 383.222_1698        | -0.242985258089082  | 0.402560883588054   | 8.504989e-04        | 1                   | 6.464336e-10        | 1.221705e-10        | 1.978970e-03        | 1.720463e-02        | \n",
       "| 20                  | 383.222_1407        | -0.0666029709839993 | 0.821029580534277   | 1.763110e-03        | 1                   | 6.464336e-10        | 1.221705e-10        | 8.650469e-10        | 6.174435e-04        | \n",
       "| 21                  | 387.216_1361        | 0.281855815198855   | 0.328930260816831   | 2.230659e-04        | 1                   | 6.464336e-10        | 1.221705e-10        | 8.650469e-10        | 3.423586e-10        | \n",
       "| 22                  | 393.166_642         | 0.228387251366747   | 0.432254605627892   | 1.115320e-04        | 1                   | 6.464336e-10        | 1.221705e-10        | 8.650469e-10        | 3.423586e-10        | \n",
       "| 23                  | 397.179_821         | 0.211307326756097   | 0.468343345973288   | 1.363555e-05        | 1                   | 1.595529e-05        | 1.221705e-10        | 2.190143e-05        | 3.423586e-10        | \n",
       "| 24                  | 397.18_672          | 0.172207640811325   | 0.556066648849158   | 4.367197e-05        | 1                   | 6.464336e-10        | 1.221705e-10        | 8.650469e-10        | 3.423586e-10        | \n",
       "| 25                  | 400.157_589         | 0.228659476892485   | 0.431691028838877   | 3.814065e-05        | 1                   | 6.464336e-10        | 1.221705e-10        | 8.650469e-10        | 3.423586e-10        | \n",
       "| 26                  | 400.175_809         | 0.225954440307934   | 0.43730753983575    | 1.236224e-04        | 1                   | 6.464336e-10        | 1.221705e-10        | 8.650469e-10        | 3.423586e-10        | \n",
       "| 27                  | 401.232_1290        | 0.911533897243834   | 5.7064270699847e-06 | 9.569529e-03        | 0.00334967269008102 | 1.960109e-05        | 2.601850e-05        | 8.650469e-10        | 5.627394e-05        | \n",
       "| 28                  | 401.232_1411        | 0.156482370780623   | 0.593185890419915   | 1.867191e-03        | 1                   | 6.464336e-10        | 1.221705e-10        | 8.650469e-10        | 3.423586e-10        | \n",
       "| 29                  | 401.232_1619        | 0.640073772749594   | 0.0136797352409133  | 1.046219e-02        | 1                   | 6.464336e-10        | 1.221705e-10        | 8.650469e-10        | 4.234155e-05        | \n",
       "| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | \n",
       "| 558                  | 868.356_1418         | -0.123916349672485   | 0.67298286230042     | 2.423684e-04         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 559                  | 869.352_941          | 0.228871589198768    | 0.431252158342323    | 5.189897e-03         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 560                  | 869.392_1670         | -0.138127625586833   | 0.637705709112937    | 1.943030e-04         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 561                  | 870.361_1433         | -0.142327465996463   | 0.627411366909868    | 2.407108e-05         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 562                  | 872.373_933          | -0.169581520797562   | 0.562196424949146    | 6.360730e-06         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 563                  | 872.373_867          | -0.17168074681055    | 0.557294227073848    | 2.448277e-05         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 564                  | 874.363_1337         | -0.0762150612440404  | 0.79566697946497     | 4.025099e-05         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 565                  | 881.32_878           | -0.0456016842842233  | 0.876981592762568    | 4.137304e-04         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 566                  | 882.33_1231          | 0.215278406255525    | 0.459826208385533    | 3.714671e-04         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 567                  | 883.33_776           | 0.22762293857456     | 0.43383890536112     | 1.134265e-03         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 568                  | 883.36_1084          | 0.226857086624798    | 0.435429313884083    | 1.049822e-03         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 569                  | 884.403_1197         | -0.19571665652726    | 0.502500080797765    | 3.416119e-05         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 570                  | 885.328_1499         | -0.140168489162022   | 0.632695569993799    | 7.163746e-04         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 571                  | 890.336_1433         | -0.173610421967432   | 0.552803995293411    | 7.736488e-05         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 572                  | 890.376_857          | -0.170642781563919   | 0.559715865190782    | 2.445946e-11         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 573                  | 891.33_941           | 0.235112721192342    | 0.418440050952477    | 2.963642e-04         | 1                    | 1.903514e-05         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 574                  | 892.407_1610         | -0.0367844701475624  | 0.900647487143874    | 2.354112e-04         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 575                  | 893.416_1609         | -0.0400530918407881  | 0.891864372574871    | 1.180280e-04         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 576                  | 894.426_1631         | 0.00495069939264375  | 0.986598849465163    | 8.715378e-05         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 577                  | 895.374_1424         | -0.0610903099469755  | 0.835650657086433    | 5.474881e-05         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 578                  | 895.407_1768         | -0.0979804586462028  | 0.738959134381491    | 6.713617e-04         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 579                  | 897.375_1333         | 0.219605705905163    | 0.450631623694371    | 2.554670e-05         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 580                  | 903.335_1024         | 0.229358628939693    | 0.430245300634323    | 7.472515e-04         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 581                  | 905.349_1085         | 0.242771404102679    | 0.40298803522669     | 2.531490e-04         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 582                  | 906.39_1200          | -0.197018302170316   | 0.499605428975835    | 4.226406e-05         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 583                  | 914.392_1610         | -0.00750358060402209 | 0.97968947879799     | 2.373081e-04         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 584                  | 916.412_1631         | 0.0473109703903092   | 0.872404223005271    | 6.811799e-05         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 585                  | 927.391_1213         | -0.171019340513868   | 0.558836817323772    | 2.445946e-11         | 1                    | 6.464336e-10         | 1.221705e-10         | 8.650469e-10         | 3.423586e-10         | \n",
       "| 586                  | 983.559_1688         | -0.185422040102229   | 0.525661291436393    | 5.060243e-04         | 1                    | 1.412577e-04         | 2.424826e-01         | 8.936452e-03         | 6.439997e-05         | \n",
       "| 587                  | 987.593_1777         | -0.179208062169923   | 0.539866703843945    | 1.229554e-05         | 1                    | 6.464336e-10         | 4.639795e-02         | 2.693216e-04         | 3.423586e-10         | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "      shared name IDs              cor                   p_value           \n",
       " [1,]             BioactivityCHIKV 0                    0                  \n",
       " [2,] 1           270.279_1698     -0.324377606725705   0.257849356719369  \n",
       " [3,] 2           271.283_1699     -0.318374649942669   0.267271199671765  \n",
       " [4,] 3           279.174_1413     0.11344978411662     0.699375059832539  \n",
       " [5,] 4           280.264_1420     -0.200702959079237   0.49145327312603   \n",
       " [6,] 5           281.19_1031      -0.201330433729144   0.490071225054009  \n",
       " [7,] 6           282.279_1660     -0.201928970163321   0.48875460960341   \n",
       " [8,] 7           297.185_1652     -0.27121389090935    0.348283666308653  \n",
       " [9,] 8           297.185_1556     -0.214874888224598   0.460688215436271  \n",
       "[10,] 9           298.311_1968     -0.296642926666024   0.3030698225754    \n",
       "[11,] 10          313.179_1721     0.514149093415966    0.0599876302308284 \n",
       "[12,] 11          315.195_1687     -0.214387381474332   0.461730687253729  \n",
       "[13,] 12          315.195_1777     -0.20372853105752    0.484806069511438  \n",
       "[14,] 13          341.267_1509     -0.2053974044361     0.481157749869592  \n",
       "[15,] 14          363.25_1511      -0.207281369412495   0.477054883790855  \n",
       "[16,] 15          383.165_564      0.229673438354267    0.42959512606125   \n",
       "[17,] 16          383.22_1668      -0.187953232291067   0.519922948532928  \n",
       "[18,] 17          383.222_1524     0.534793863828435    0.0487932731059066 \n",
       "[19,] 18          383.222_1615     -0.037574232106698   0.898524312804278  \n",
       "[20,] 19          383.222_1698     -0.242985258089082   0.402560883588054  \n",
       "[21,] 20          383.222_1407     -0.0666029709839993  0.821029580534277  \n",
       "[22,] 21          387.216_1361     0.281855815198855    0.328930260816831  \n",
       "[23,] 22          393.166_642      0.228387251366747    0.432254605627892  \n",
       "[24,] 23          397.179_821      0.211307326756097    0.468343345973288  \n",
       "[25,] 24          397.18_672       0.172207640811325    0.556066648849158  \n",
       "[26,] 25          400.157_589      0.228659476892485    0.431691028838877  \n",
       "[27,] 26          400.175_809      0.225954440307934    0.43730753983575   \n",
       "[28,] 27          401.232_1290     0.911533897243834    5.7064270699847e-06\n",
       "[29,] 28          401.232_1411     0.156482370780623    0.593185890419915  \n",
       "[30,] 29          401.232_1619     0.640073772749594    0.0136797352409133 \n",
       "[31,] ⋮           ⋮                ⋮                    ⋮                  \n",
       "[32,] 558         868.356_1418     -0.123916349672485   0.67298286230042   \n",
       "[33,] 559         869.352_941      0.228871589198768    0.431252158342323  \n",
       "[34,] 560         869.392_1670     -0.138127625586833   0.637705709112937  \n",
       "[35,] 561         870.361_1433     -0.142327465996463   0.627411366909868  \n",
       "[36,] 562         872.373_933      -0.169581520797562   0.562196424949146  \n",
       "[37,] 563         872.373_867      -0.17168074681055    0.557294227073848  \n",
       "[38,] 564         874.363_1337     -0.0762150612440404  0.79566697946497   \n",
       "[39,] 565         881.32_878       -0.0456016842842233  0.876981592762568  \n",
       "[40,] 566         882.33_1231      0.215278406255525    0.459826208385533  \n",
       "[41,] 567         883.33_776       0.22762293857456     0.43383890536112   \n",
       "[42,] 568         883.36_1084      0.226857086624798    0.435429313884083  \n",
       "[43,] 569         884.403_1197     -0.19571665652726    0.502500080797765  \n",
       "[44,] 570         885.328_1499     -0.140168489162022   0.632695569993799  \n",
       "[45,] 571         890.336_1433     -0.173610421967432   0.552803995293411  \n",
       "[46,] 572         890.376_857      -0.170642781563919   0.559715865190782  \n",
       "[47,] 573         891.33_941       0.235112721192342    0.418440050952477  \n",
       "[48,] 574         892.407_1610     -0.0367844701475624  0.900647487143874  \n",
       "[49,] 575         893.416_1609     -0.0400530918407881  0.891864372574871  \n",
       "[50,] 576         894.426_1631     0.00495069939264375  0.986598849465163  \n",
       "[51,] 577         895.374_1424     -0.0610903099469755  0.835650657086433  \n",
       "[52,] 578         895.407_1768     -0.0979804586462028  0.738959134381491  \n",
       "[53,] 579         897.375_1333     0.219605705905163    0.450631623694371  \n",
       "[54,] 580         903.335_1024     0.229358628939693    0.430245300634323  \n",
       "[55,] 581         905.349_1085     0.242771404102679    0.40298803522669   \n",
       "[56,] 582         906.39_1200      -0.197018302170316   0.499605428975835  \n",
       "[57,] 583         914.392_1610     -0.00750358060402209 0.97968947879799   \n",
       "[58,] 584         916.412_1631     0.0473109703903092   0.872404223005271  \n",
       "[59,] 585         927.391_1213     -0.171019340513868   0.558836817323772  \n",
       "[60,] 586         983.559_1688     -0.185422040102229   0.525661291436393  \n",
       "[61,] 587         987.593_1777     -0.179208062169923   0.539866703843945  \n",
       "      Extract      p_value_corrected   F_5          F_6          F_7         \n",
       " [1,]  68.0        0                     1.0          4.0          1.0       \n",
       " [2,] 0.0001391824 1                   0.1594079650 0.0228397314 0.3139762067\n",
       " [3,] 0.0000139267 1                   0.0261136500 0.0037518603 0.0552725554\n",
       " [4,] 7.760803e-05 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       " [5,] 4.456230e-05 1                   6.101911e-02 8.258893e-05 8.404894e-05\n",
       " [6,] 4.369353e-05 1                   6.464336e-10 1.194904e-04 2.992650e-02\n",
       " [7,] 4.563084e-04 1                   5.618968e-01 1.014960e-03 2.860098e-03\n",
       " [8,] 6.741464e-05 1                   6.464336e-10 1.150745e-02 8.201229e-03\n",
       " [9,] 3.286022e-04 1                   6.464336e-10 4.233761e-03 5.458206e-02\n",
       "[10,] 2.040302e-05 1                   2.699247e-02 6.353464e-03 7.801129e-02\n",
       "[11,] 8.948249e-04 1                   6.464336e-10 2.849181e-04 2.773147e-04\n",
       "[12,] 6.075624e-04 1                   6.464336e-10 1.445606e-01 2.564659e-02\n",
       "[13,] 9.569474e-05 1                   7.234580e-05 2.708920e-02 3.310437e-03\n",
       "[14,] 1.669249e-05 1                   6.464336e-10 1.221705e-10 1.456070e-03\n",
       "[15,] 8.686752e-06 1                   6.464336e-10 1.221705e-10 1.449499e-03\n",
       "[16,] 8.354078e-05 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[17,] 4.680118e-04 1                   1.962724e-05 3.305265e-06 8.650469e-10\n",
       "[18,] 7.535002e-04 1                   6.464336e-10 6.433913e-06 8.650469e-10\n",
       "[19,] 3.551571e-03 1                   1.517113e-05 6.781142e-06 8.650469e-10\n",
       "[20,] 8.504989e-04 1                   6.464336e-10 1.221705e-10 1.978970e-03\n",
       "[21,] 1.763110e-03 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[22,] 2.230659e-04 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[23,] 1.115320e-04 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[24,] 1.363555e-05 1                   1.595529e-05 1.221705e-10 2.190143e-05\n",
       "[25,] 4.367197e-05 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[26,] 3.814065e-05 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[27,] 1.236224e-04 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[28,] 9.569529e-03 0.00334967269008102 1.960109e-05 2.601850e-05 8.650469e-10\n",
       "[29,] 1.867191e-03 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[30,] 1.046219e-02 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[31,] ⋮            ⋮                   ⋮            ⋮            ⋮           \n",
       "[32,] 2.423684e-04 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[33,] 5.189897e-03 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[34,] 1.943030e-04 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[35,] 2.407108e-05 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[36,] 6.360730e-06 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[37,] 2.448277e-05 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[38,] 4.025099e-05 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[39,] 4.137304e-04 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[40,] 3.714671e-04 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[41,] 1.134265e-03 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[42,] 1.049822e-03 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[43,] 3.416119e-05 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[44,] 7.163746e-04 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[45,] 7.736488e-05 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[46,] 2.445946e-11 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[47,] 2.963642e-04 1                   1.903514e-05 1.221705e-10 8.650469e-10\n",
       "[48,] 2.354112e-04 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[49,] 1.180280e-04 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[50,] 8.715378e-05 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[51,] 5.474881e-05 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[52,] 6.713617e-04 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[53,] 2.554670e-05 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[54,] 7.472515e-04 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[55,] 2.531490e-04 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[56,] 4.226406e-05 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[57,] 2.373081e-04 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[58,] 6.811799e-05 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[59,] 2.445946e-11 1                   6.464336e-10 1.221705e-10 8.650469e-10\n",
       "[60,] 5.060243e-04 1                   1.412577e-04 2.424826e-01 8.936452e-03\n",
       "[61,] 1.229554e-05 1                   6.464336e-10 4.639795e-02 2.693216e-04\n",
       "      F_8         \n",
       " [1,]   3.0       \n",
       " [2,] 0.0551088883\n",
       " [3,] 0.0090100816\n",
       " [4,] 3.423586e-10\n",
       " [5,] 5.121893e-05\n",
       " [6,] 8.518229e-05\n",
       " [7,] 9.171837e-04\n",
       " [8,] 7.540400e-05\n",
       " [9,] 4.329827e-04\n",
       "[10,] 7.468284e-03\n",
       "[11,] 1.615254e-05\n",
       "[12,] 1.606978e-03\n",
       "[13,] 1.601149e-04\n",
       "[14,] 1.487605e-02\n",
       "[15,] 1.355859e-02\n",
       "[16,] 3.423586e-10\n",
       "[17,] 1.703802e-02\n",
       "[18,] 1.937745e-04\n",
       "[19,] 3.491533e-03\n",
       "[20,] 1.720463e-02\n",
       "[21,] 6.174435e-04\n",
       "[22,] 3.423586e-10\n",
       "[23,] 3.423586e-10\n",
       "[24,] 3.423586e-10\n",
       "[25,] 3.423586e-10\n",
       "[26,] 3.423586e-10\n",
       "[27,] 3.423586e-10\n",
       "[28,] 5.627394e-05\n",
       "[29,] 3.423586e-10\n",
       "[30,] 4.234155e-05\n",
       "[31,] ⋮           \n",
       "[32,] 3.423586e-10\n",
       "[33,] 3.423586e-10\n",
       "[34,] 3.423586e-10\n",
       "[35,] 3.423586e-10\n",
       "[36,] 3.423586e-10\n",
       "[37,] 3.423586e-10\n",
       "[38,] 3.423586e-10\n",
       "[39,] 3.423586e-10\n",
       "[40,] 3.423586e-10\n",
       "[41,] 3.423586e-10\n",
       "[42,] 3.423586e-10\n",
       "[43,] 3.423586e-10\n",
       "[44,] 3.423586e-10\n",
       "[45,] 3.423586e-10\n",
       "[46,] 3.423586e-10\n",
       "[47,] 3.423586e-10\n",
       "[48,] 3.423586e-10\n",
       "[49,] 3.423586e-10\n",
       "[50,] 3.423586e-10\n",
       "[51,] 3.423586e-10\n",
       "[52,] 3.423586e-10\n",
       "[53,] 3.423586e-10\n",
       "[54,] 3.423586e-10\n",
       "[55,] 3.423586e-10\n",
       "[56,] 3.423586e-10\n",
       "[57,] 3.423586e-10\n",
       "[58,] 3.423586e-10\n",
       "[59,] 3.423586e-10\n",
       "[60,] 6.439997e-05\n",
       "[61,] 3.423586e-10"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Prepare the new table\n",
    "new <- cbind(new[,1:5], c(0, p.adjust(as.numeric(ct[-c(1:2),2]), method = \"bonferroni\")), new[,-c(1:5)])\n",
    "colnames(new)[6] <- \"p_value_corrected\"\n",
    "new[,1:10]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# Write the final table with corrected p_value\n",
    "write.csv(new, \"features_quantification_matrix_transposed_with_significant_correlation_pvalue_corrected.csv\", row.names=FALSE)"
   ]
  }
 ],
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