removed original notebook (to be replced by Colab Notebook)

1 files changed, 0 insertions, 949 deletions

diff --git a/covid_2019_competition_results.ipynb b/covid_2019_competition_results.ipynb
deleted file mode 100644
index c8ffecb..0000000
--- a/covid_2019_competition_results.ipynb
+++ /dev/null
@@ -1,949 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Using Connectivity map data and PharmacoGx R package to find drugs against coronaviruses"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Connectivity map or Cmap is resource that uses gene expression data to connect disease transcriptomic signature with those of different types of cells after drug treatment. If the transcriptomic signature of a drug on cell line is opposite from disease signature, it can be expected that this drug could have a positive effect on amelioration of disease.\n",
-    "\n",
-    "\n",
-    "References:\n",
-    "Subramanian A, et al. A Next Generation Connectivity Map: L1000 Platform And The First 1,000,000 Profiles. Cell. 2017/12/1. 171(6):1437–1452.\n",
-    "\n",
-    "Lamb J, et al. The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science. 2006/9/29. 313(5795):1929-35, (2006)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Harmonizome is a collection of processed datasets from over 70 major online resources. I downloaded from Harmonizome \"GEO Signatures of Differentially Expressed Genes for Viral Infections\". For this analysis I used transcriptomics data of lungs from mice that were infected with icSARS CoV (GEO accesion number GSE50000;7th day of infection) and Calu-3 2B4 cells that were infected with Human Coronavirus EMC 2012 (GEO accession number GSE45042;24 hours after infection). For this analysis I havent used transcriptomic data of novel human coronavirus 2019 or SARS-2, but according to the literature all of these viruses (MERS,SARS1 and SARS2) are betacoronaviruses that have origin in bats and SARS-2 is shown to be very similar to SARS-01 according to phylogenic analysis. \n",
-    "\n",
-    "References:\n",
-    "Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma'ayan A. The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database (Oxford). 2016 Jul 3;2016. pii: baw100.\n",
-    "\t\n",
-    "Josset L, Menachery VD, Gralinski LE, Agnihothram S et al. Cell host response to infection with novel human coronavirus EMC predicts potential antivirals and important differences with SARS coronavirus. mBio 2013 Apr 30;4(3):e00165-13. PMID: 23631916\n",
-    "\n",
-    "Menachery VD, Eisfeld AJ, Schäfer A, Josset L et al. Pathogenic influenza viruses and coronaviruses utilize similar and contrasting approaches to control interferon-stimulated gene responses. mBio 2014 May 20;5(3):e01174-14. PMID: 24846384\n",
-    "\n",
-    "Yushun Wan, Jian Shang, Rachel Graham, Ralph S. Baric, Fang Li. Receptor recognition by novel coronavirus from Wuhan: An analysis based on decade-long structural studies of SARS. Journal of Virology, 2020; DOI: 10.1128/JVI.00127-20\n",
-    "\n",
-    "Yadi Zhou, Yuan Hou, Jiayu Shen, Yin Huang, William Martin, Feixiong Cheng.Network-based Drug Repurposing for Human Coronavirus\n",
-    "doi: https://doi.org/10.1101/2020.02.03.20020263"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "For the analysis of Connectivity map data I used PharmacoGx R package.\n",
-    "\n",
-    "P Smirnov, Z Safikhani, N El-Hachem , D Wang, A She , C Olsen, MFreeman, H Selby, D Gendoo , P Grossman , A Beck , H Aerts ,\n",
-    "M Lupien, A Goldenberg ,B Haibe-Kains PharmacoGx: an R package for analysis of large pharmacogenomic datasets Bioinformatics (2016)."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 76,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "library(PharmacoGx)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 77,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<table>\n",
-       "<caption>A data.frame: 11 × 5</caption>\n",
-       "<thead>\n",
-       "\t<tr><th></th><th scope=col>PSet.Name</th><th scope=col>Dataset.Type</th><th scope=col>Available.Molecular.Profiles</th><th scope=col>Date.Updated</th><th scope=col>URL</th></tr>\n",
-       "\t<tr><th></th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;fct&gt;</th></tr>\n",
-       "</thead>\n",
-       "<tbody>\n",
-       "\t<tr><th scope=row>CCLE_2013</th><td>CCLE_2013      </td><td>sensitivity </td><td>rna/mutation                </td><td>Tue Sep 15 18:50:07 2015</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CCLE_Nature2013.RData</td></tr>\n",
-       "\t<tr><th scope=row>CCLE</th><td>CCLE           </td><td>sensitivity </td><td>rna/rnaseq/mutation/cnv     </td><td>Thu Dec 10 18:17:14 2015</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CCLE.RData           </td></tr>\n",
-       "\t<tr><th scope=row>GDSC_2013</th><td>GDSC_2013      </td><td>sensitivity </td><td>rna/mutation                </td><td>Mon Oct  5 16:07:54 2015</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CGP_Nature2013.RData </td></tr>\n",
-       "\t<tr><th scope=row>GDSC</th><td>GDSC           </td><td>sensitivity </td><td>rna/rna2/mutation/fusion/cnv</td><td>Wed Dec 30 10:44:21 2015</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/GDSC.RData           </td></tr>\n",
-       "\t<tr><th scope=row>GDSC1000</th><td>GDSC1000       </td><td>sensitivity </td><td>rna                         </td><td>Thu Aug 25 11:13:00 2016</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/GDSC1000.RData       </td></tr>\n",
-       "\t<tr><th scope=row>gCSI</th><td>gCSI           </td><td>sensitivity </td><td>rnaseq/cnv                  </td><td>Mon Jun 13 18:50:12 2016</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/gCSI.RData           </td></tr>\n",
-       "\t<tr><th scope=row>FIMM</th><td>FIMM           </td><td>sensitivity </td><td>                            </td><td>Mon Oct 3 17:14:00 2016 </td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/FIMM.RData           </td></tr>\n",
-       "\t<tr><th scope=row>CTRPv2</th><td>CTRPv2         </td><td>sensitivity </td><td>                            </td><td>Thu Aug 25 11:15:00 2016</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CTRPv2.RData         </td></tr>\n",
-       "\t<tr><th scope=row>CMAP</th><td>CMAP           </td><td>perturbation</td><td>rna                         </td><td>Mon Sep 21 02:38:45 2015</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CMAP.RData           </td></tr>\n",
-       "\t<tr><th scope=row>L1000_compounds</th><td>L1000_compounds</td><td>perturbation</td><td>rna                         </td><td>Mon Jan 25 12:51:00 2016</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/L1000_compounds.RData</td></tr>\n",
-       "\t<tr><th scope=row>L1000_genetic</th><td>L1000_genetic  </td><td>perturbation</td><td>rna                         </td><td>Mon Jan 25 12:51:00 2016</td><td>https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/L1000_genetic.RData  </td></tr>\n",
-       "</tbody>\n",
-       "</table>\n"
-      ],
-      "text/latex": [
-       "A data.frame: 11 × 5\n",
-       "\\begin{tabular}{r|lllll}\n",
-       "  & PSet.Name & Dataset.Type & Available.Molecular.Profiles & Date.Updated & URL\\\\\n",
-       "  & <fct> & <fct> & <fct> & <fct> & <fct>\\\\\n",
-       "\\hline\n",
-       "\tCCLE\\_2013 & CCLE\\_2013       & sensitivity  & rna/mutation                 & Tue Sep 15 18:50:07 2015 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CCLE\\_Nature2013.RData\\\\\n",
-       "\tCCLE & CCLE            & sensitivity  & rna/rnaseq/mutation/cnv      & Thu Dec 10 18:17:14 2015 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CCLE.RData           \\\\\n",
-       "\tGDSC\\_2013 & GDSC\\_2013       & sensitivity  & rna/mutation                 & Mon Oct  5 16:07:54 2015 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CGP\\_Nature2013.RData \\\\\n",
-       "\tGDSC & GDSC            & sensitivity  & rna/rna2/mutation/fusion/cnv & Wed Dec 30 10:44:21 2015 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/GDSC.RData           \\\\\n",
-       "\tGDSC1000 & GDSC1000        & sensitivity  & rna                          & Thu Aug 25 11:13:00 2016 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/GDSC1000.RData       \\\\\n",
-       "\tgCSI & gCSI            & sensitivity  & rnaseq/cnv                   & Mon Jun 13 18:50:12 2016 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/gCSI.RData           \\\\\n",
-       "\tFIMM & FIMM            & sensitivity  &                              & Mon Oct 3 17:14:00 2016  & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/FIMM.RData           \\\\\n",
-       "\tCTRPv2 & CTRPv2          & sensitivity  &                              & Thu Aug 25 11:15:00 2016 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CTRPv2.RData         \\\\\n",
-       "\tCMAP & CMAP            & perturbation & rna                          & Mon Sep 21 02:38:45 2015 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CMAP.RData           \\\\\n",
-       "\tL1000\\_compounds & L1000\\_compounds & perturbation & rna                          & Mon Jan 25 12:51:00 2016 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/L1000\\_compounds.RData\\\\\n",
-       "\tL1000\\_genetic & L1000\\_genetic   & perturbation & rna                          & Mon Jan 25 12:51:00 2016 & https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/L1000\\_genetic.RData  \\\\\n",
-       "\\end{tabular}\n"
-      ],
-      "text/markdown": [
-       "\n",
-       "A data.frame: 11 × 5\n",
-       "\n",
-       "| <!--/--> | PSet.Name &lt;fct&gt; | Dataset.Type &lt;fct&gt; | Available.Molecular.Profiles &lt;fct&gt; | Date.Updated &lt;fct&gt; | URL &lt;fct&gt; |\n",
-       "|---|---|---|---|---|---|\n",
-       "| CCLE_2013 | CCLE_2013       | sensitivity  | rna/mutation                 | Tue Sep 15 18:50:07 2015 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CCLE_Nature2013.RData |\n",
-       "| CCLE | CCLE            | sensitivity  | rna/rnaseq/mutation/cnv      | Thu Dec 10 18:17:14 2015 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CCLE.RData            |\n",
-       "| GDSC_2013 | GDSC_2013       | sensitivity  | rna/mutation                 | Mon Oct  5 16:07:54 2015 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CGP_Nature2013.RData  |\n",
-       "| GDSC | GDSC            | sensitivity  | rna/rna2/mutation/fusion/cnv | Wed Dec 30 10:44:21 2015 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/GDSC.RData            |\n",
-       "| GDSC1000 | GDSC1000        | sensitivity  | rna                          | Thu Aug 25 11:13:00 2016 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/GDSC1000.RData        |\n",
-       "| gCSI | gCSI            | sensitivity  | rnaseq/cnv                   | Mon Jun 13 18:50:12 2016 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/gCSI.RData            |\n",
-       "| FIMM | FIMM            | sensitivity  | <!----> | Mon Oct 3 17:14:00 2016  | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/FIMM.RData            |\n",
-       "| CTRPv2 | CTRPv2          | sensitivity  | <!----> | Thu Aug 25 11:15:00 2016 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CTRPv2.RData          |\n",
-       "| CMAP | CMAP            | perturbation | rna                          | Mon Sep 21 02:38:45 2015 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CMAP.RData            |\n",
-       "| L1000_compounds | L1000_compounds | perturbation | rna                          | Mon Jan 25 12:51:00 2016 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/L1000_compounds.RData |\n",
-       "| L1000_genetic | L1000_genetic   | perturbation | rna                          | Mon Jan 25 12:51:00 2016 | https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/L1000_genetic.RData   |\n",
-       "\n"
-      ],
-      "text/plain": [
-       "                PSet.Name       Dataset.Type Available.Molecular.Profiles\n",
-       "CCLE_2013       CCLE_2013       sensitivity  rna/mutation                \n",
-       "CCLE            CCLE            sensitivity  rna/rnaseq/mutation/cnv     \n",
-       "GDSC_2013       GDSC_2013       sensitivity  rna/mutation                \n",
-       "GDSC            GDSC            sensitivity  rna/rna2/mutation/fusion/cnv\n",
-       "GDSC1000        GDSC1000        sensitivity  rna                         \n",
-       "gCSI            gCSI            sensitivity  rnaseq/cnv                  \n",
-       "FIMM            FIMM            sensitivity                              \n",
-       "CTRPv2          CTRPv2          sensitivity                              \n",
-       "CMAP            CMAP            perturbation rna                         \n",
-       "L1000_compounds L1000_compounds perturbation rna                         \n",
-       "L1000_genetic   L1000_genetic   perturbation rna                         \n",
-       "                Date.Updated            \n",
-       "CCLE_2013       Tue Sep 15 18:50:07 2015\n",
-       "CCLE            Thu Dec 10 18:17:14 2015\n",
-       "GDSC_2013       Mon Oct  5 16:07:54 2015\n",
-       "GDSC            Wed Dec 30 10:44:21 2015\n",
-       "GDSC1000        Thu Aug 25 11:13:00 2016\n",
-       "gCSI            Mon Jun 13 18:50:12 2016\n",
-       "FIMM            Mon Oct 3 17:14:00 2016 \n",
-       "CTRPv2          Thu Aug 25 11:15:00 2016\n",
-       "CMAP            Mon Sep 21 02:38:45 2015\n",
-       "L1000_compounds Mon Jan 25 12:51:00 2016\n",
-       "L1000_genetic   Mon Jan 25 12:51:00 2016\n",
-       "                URL                                                                                 \n",
-       "CCLE_2013       https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CCLE_Nature2013.RData\n",
-       "CCLE            https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CCLE.RData           \n",
-       "GDSC_2013       https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CGP_Nature2013.RData \n",
-       "GDSC            https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/GDSC.RData           \n",
-       "GDSC1000        https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/GDSC1000.RData       \n",
-       "gCSI            https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/gCSI.RData           \n",
-       "FIMM            https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/FIMM.RData           \n",
-       "CTRPv2          https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CTRPv2.RData         \n",
-       "CMAP            https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/CMAP.RData           \n",
-       "L1000_compounds https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/L1000_compounds.RData\n",
-       "L1000_genetic   https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/L1000_genetic.RData  "
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "availablePSets()\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 78,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "CMAP.sigs <- downloadPertSig(\"CMAP\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 80,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    " drug.perturbation <- CMAP.sigs"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 82,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "sars1_up_and_down_genes <-read.csv(\"icSARS_Cov_Day7_None_GSE50000.csv\",stringsAsFactors = F, header = T, sep=\";\")\n",
-    "rownames(sars1_up_and_down_genes) <- sars1_up_and_down_genes$Feature\n",
-    "sars1<- sars1_up_and_down_genes$Direction\n",
-    "names(sars1) <- rownames(sars1_up_and_down_genes)\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 83,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "res_sars1 <- apply(drug.perturbation[,,c(\"tstat\", \"fdr\")], \n",
-    "             2,function(x, sars1){\n",
-    "         return(connectivityScore(x=x, \n",
-    "                                  y=sars1,\n",
-    "                               method=\"fgsea\", nperm=100))\n",
-    "       },sars1 = sars1)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 84,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<style>\n",
-       ".list-inline {list-style: none; margin:0; padding: 0}\n",
-       ".list-inline>li {display: inline-block}\n",
-       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
-       "</style>\n",
-       "<ol class=list-inline><li>'Connectivity'</li><li>'P_value'</li></ol>\n"
-      ],
-      "text/latex": [
-       "\\begin{enumerate*}\n",
-       "\\item 'Connectivity'\n",
-       "\\item 'P\\_value'\n",
-       "\\end{enumerate*}\n"
-      ],
-      "text/markdown": [
-       "1. 'Connectivity'\n",
-       "2. 'P_value'\n",
-       "\n",
-       "\n"
-      ],
-      "text/plain": [
-       "[1] \"Connectivity\" \"P_value\"     "
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "rownames(res_sars1) <- c(\"Connectivity\", \"P_value\")\n",
-    "res_sars1 <- t(res_sars1)\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 95,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "con_score_sars <-res_sars1[order((res_sars1[,1]),decreasing = F),]\n",
-    "p_value_sars <- res_sars1[order((res_sars1[,2]),decreasing = F),]"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 96,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<table>\n",
-       "<caption>A matrix: 1288 × 2 of type dbl</caption>\n",
-       "<thead>\n",
-       "\t<tr><th></th><th scope=col>Connectivity</th><th scope=col>P_value</th></tr>\n",
-       "</thead>\n",
-       "<tbody>\n",
-       "\t<tr><th scope=row>valproic acid</th><td>-0.376625</td><td>0.003243431</td></tr>\n",
-       "\t<tr><th scope=row>rifabutin</th><td>-0.340380</td><td>0.003249652</td></tr>\n",
-       "\t<tr><th scope=row>levomepromazine</th><td>-0.329905</td><td>0.003363063</td></tr>\n",
-       "\t<tr><th scope=row>promazine</th><td>-0.338460</td><td>0.003408985</td></tr>\n",
-       "\t<tr><th scope=row>Prestwick-559</th><td>-0.332285</td><td>0.003453743</td></tr>\n",
-       "\t<tr><th scope=row>maprotiline</th><td>-0.345995</td><td>0.003483930</td></tr>\n",
-       "\t<tr><th scope=row>nicergoline</th><td>-0.297975</td><td>0.003540995</td></tr>\n",
-       "\t<tr><th scope=row>GW-8510</th><td>-0.365775</td><td>0.003643482</td></tr>\n",
-       "\t<tr><th scope=row>lasalocid</th><td>-0.287965</td><td>0.003653011</td></tr>\n",
-       "\t<tr><th scope=row>pyrvinium</th><td>-0.312920</td><td>0.003692544</td></tr>\n",
-       "\t<tr><th scope=row>nortriptyline</th><td>-0.346990</td><td>0.003785772</td></tr>\n",
-       "\t<tr><th scope=row>prochlorperazine</th><td>-0.360245</td><td>0.003809080</td></tr>\n",
-       "\t<tr><th scope=row>norcyclobenzaprine</th><td>-0.319960</td><td>0.003935323</td></tr>\n",
-       "\t<tr><th scope=row>fluphenazine</th><td>-0.351740</td><td>0.004089757</td></tr>\n",
-       "\t<tr><th scope=row>LY-294002</th><td>-0.358135</td><td>0.004118938</td></tr>\n",
-       "\t<tr><th scope=row>raloxifene</th><td>-0.301795</td><td>0.004218595</td></tr>\n",
-       "\t<tr><th scope=row>4,5-dianilinophthalimide</th><td>-0.809330</td><td>0.006282675</td></tr>\n",
-       "\t<tr><th scope=row>trichostatin A</th><td>-0.330245</td><td>0.006335983</td></tr>\n",
-       "\t<tr><th scope=row>eucatropine</th><td>-0.288555</td><td>0.006421429</td></tr>\n",
-       "\t<tr><th scope=row>syrosingopine</th><td>-0.318895</td><td>0.006459413</td></tr>\n",
-       "\t<tr><th scope=row>mebendazole</th><td>-0.300325</td><td>0.006618701</td></tr>\n",
-       "\t<tr><th scope=row>lycorine</th><td> 0.319895</td><td>0.006644780</td></tr>\n",
-       "\t<tr><th scope=row>rescinnamine</th><td>-0.323295</td><td>0.006987249</td></tr>\n",
-       "\t<tr><th scope=row>reserpine</th><td>-0.285080</td><td>0.007184183</td></tr>\n",
-       "\t<tr><th scope=row>sirolimus</th><td>-0.361685</td><td>0.007393165</td></tr>\n",
-       "\t<tr><th scope=row>trifluoperazine</th><td>-0.375195</td><td>0.007405285</td></tr>\n",
-       "\t<tr><th scope=row>vorinostat</th><td>-0.378310</td><td>0.008683363</td></tr>\n",
-       "\t<tr><th scope=row>methotrexate</th><td>-0.336405</td><td>0.008864197</td></tr>\n",
-       "\t<tr><th scope=row>fulvestrant</th><td>-0.281245</td><td>0.009065718</td></tr>\n",
-       "\t<tr><th scope=row>phenazopyridine</th><td>-0.321425</td><td>0.009136916</td></tr>\n",
-       "\t<tr><th scope=row>...</th><td>...</td><td>...</td></tr>\n",
-       "\t<tr><th scope=row>PF-00562151-00</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>pioglitazone</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>PF-00539745-00</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>valdecoxib</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>PF-00539758-00</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>orlistat</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>5707885</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>C-75</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>5155877</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>dinoprostone</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>5194442</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>AG-028671</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>6-bromoindirubin-3'-oxime</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>Gly-His-Lys</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>STOCK1N-35696</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>STOCK1N-28457</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>H-89</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>SB-202190</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>NS-398</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>SB-203580</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>AH-6809</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>alsterpaullone</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>SC-19220</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>0198306-0000</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>AR-A014418</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>semustine</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>CP-944629</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>irinotecan</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>BCB000039</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>11-deoxy-16,16-dimethylprostaglandin E2</th><td>0</td><td>1</td></tr>\n",
-       "</tbody>\n",
-       "</table>\n"
-      ],
-      "text/latex": [
-       "A matrix: 1288 × 2 of type dbl\n",
-       "\\begin{tabular}{r|ll}\n",
-       "  & Connectivity & P\\_value\\\\\n",
-       "\\hline\n",
-       "\tvalproic acid & -0.376625 & 0.003243431\\\\\n",
-       "\trifabutin & -0.340380 & 0.003249652\\\\\n",
-       "\tlevomepromazine & -0.329905 & 0.003363063\\\\\n",
-       "\tpromazine & -0.338460 & 0.003408985\\\\\n",
-       "\tPrestwick-559 & -0.332285 & 0.003453743\\\\\n",
-       "\tmaprotiline & -0.345995 & 0.003483930\\\\\n",
-       "\tnicergoline & -0.297975 & 0.003540995\\\\\n",
-       "\tGW-8510 & -0.365775 & 0.003643482\\\\\n",
-       "\tlasalocid & -0.287965 & 0.003653011\\\\\n",
-       "\tpyrvinium & -0.312920 & 0.003692544\\\\\n",
-       "\tnortriptyline & -0.346990 & 0.003785772\\\\\n",
-       "\tprochlorperazine & -0.360245 & 0.003809080\\\\\n",
-       "\tnorcyclobenzaprine & -0.319960 & 0.003935323\\\\\n",
-       "\tfluphenazine & -0.351740 & 0.004089757\\\\\n",
-       "\tLY-294002 & -0.358135 & 0.004118938\\\\\n",
-       "\traloxifene & -0.301795 & 0.004218595\\\\\n",
-       "\t4,5-dianilinophthalimide & -0.809330 & 0.006282675\\\\\n",
-       "\ttrichostatin A & -0.330245 & 0.006335983\\\\\n",
-       "\teucatropine & -0.288555 & 0.006421429\\\\\n",
-       "\tsyrosingopine & -0.318895 & 0.006459413\\\\\n",
-       "\tmebendazole & -0.300325 & 0.006618701\\\\\n",
-       "\tlycorine &  0.319895 & 0.006644780\\\\\n",
-       "\trescinnamine & -0.323295 & 0.006987249\\\\\n",
-       "\treserpine & -0.285080 & 0.007184183\\\\\n",
-       "\tsirolimus & -0.361685 & 0.007393165\\\\\n",
-       "\ttrifluoperazine & -0.375195 & 0.007405285\\\\\n",
-       "\tvorinostat & -0.378310 & 0.008683363\\\\\n",
-       "\tmethotrexate & -0.336405 & 0.008864197\\\\\n",
-       "\tfulvestrant & -0.281245 & 0.009065718\\\\\n",
-       "\tphenazopyridine & -0.321425 & 0.009136916\\\\\n",
-       "\t... & ... & ...\\\\\n",
-       "\tPF-00562151-00 & 0 & 1\\\\\n",
-       "\tpioglitazone & 0 & 1\\\\\n",
-       "\tPF-00539745-00 & 0 & 1\\\\\n",
-       "\tvaldecoxib & 0 & 1\\\\\n",
-       "\tPF-00539758-00 & 0 & 1\\\\\n",
-       "\torlistat & 0 & 1\\\\\n",
-       "\t5707885 & 0 & 1\\\\\n",
-       "\tC-75 & 0 & 1\\\\\n",
-       "\t5155877 & 0 & 1\\\\\n",
-       "\tdinoprostone & 0 & 1\\\\\n",
-       "\t5194442 & 0 & 1\\\\\n",
-       "\tAG-028671 & 0 & 1\\\\\n",
-       "\t6-bromoindirubin-3'-oxime & 0 & 1\\\\\n",
-       "\tGly-His-Lys & 0 & 1\\\\\n",
-       "\tSTOCK1N-35696 & 0 & 1\\\\\n",
-       "\tSTOCK1N-28457 & 0 & 1\\\\\n",
-       "\tH-89 & 0 & 1\\\\\n",
-       "\tSB-202190 & 0 & 1\\\\\n",
-       "\tNS-398 & 0 & 1\\\\\n",
-       "\tSB-203580 & 0 & 1\\\\\n",
-       "\tAH-6809 & 0 & 1\\\\\n",
-       "\talsterpaullone & 0 & 1\\\\\n",
-       "\tSC-19220 & 0 & 1\\\\\n",
-       "\t0198306-0000 & 0 & 1\\\\\n",
-       "\tAR-A014418 & 0 & 1\\\\\n",
-       "\tsemustine & 0 & 1\\\\\n",
-       "\tCP-944629 & 0 & 1\\\\\n",
-       "\tirinotecan & 0 & 1\\\\\n",
-       "\tBCB000039 & 0 & 1\\\\\n",
-       "\t11-deoxy-16,16-dimethylprostaglandin E2 & 0 & 1\\\\\n",
-       "\\end{tabular}\n"
-      ],
-      "text/markdown": [
-       "\n",
-       "A matrix: 1288 × 2 of type dbl\n",
-       "\n",
-       "| <!--/--> | Connectivity | P_value |\n",
-       "|---|---|---|\n",
-       "| valproic acid | -0.376625 | 0.003243431 |\n",
-       "| rifabutin | -0.340380 | 0.003249652 |\n",
-       "| levomepromazine | -0.329905 | 0.003363063 |\n",
-       "| promazine | -0.338460 | 0.003408985 |\n",
-       "| Prestwick-559 | -0.332285 | 0.003453743 |\n",
-       "| maprotiline | -0.345995 | 0.003483930 |\n",
-       "| nicergoline | -0.297975 | 0.003540995 |\n",
-       "| GW-8510 | -0.365775 | 0.003643482 |\n",
-       "| lasalocid | -0.287965 | 0.003653011 |\n",
-       "| pyrvinium | -0.312920 | 0.003692544 |\n",
-       "| nortriptyline | -0.346990 | 0.003785772 |\n",
-       "| prochlorperazine | -0.360245 | 0.003809080 |\n",
-       "| norcyclobenzaprine | -0.319960 | 0.003935323 |\n",
-       "| fluphenazine | -0.351740 | 0.004089757 |\n",
-       "| LY-294002 | -0.358135 | 0.004118938 |\n",
-       "| raloxifene | -0.301795 | 0.004218595 |\n",
-       "| 4,5-dianilinophthalimide | -0.809330 | 0.006282675 |\n",
-       "| trichostatin A | -0.330245 | 0.006335983 |\n",
-       "| eucatropine | -0.288555 | 0.006421429 |\n",
-       "| syrosingopine | -0.318895 | 0.006459413 |\n",
-       "| mebendazole | -0.300325 | 0.006618701 |\n",
-       "| lycorine |  0.319895 | 0.006644780 |\n",
-       "| rescinnamine | -0.323295 | 0.006987249 |\n",
-       "| reserpine | -0.285080 | 0.007184183 |\n",
-       "| sirolimus | -0.361685 | 0.007393165 |\n",
-       "| trifluoperazine | -0.375195 | 0.007405285 |\n",
-       "| vorinostat | -0.378310 | 0.008683363 |\n",
-       "| methotrexate | -0.336405 | 0.008864197 |\n",
-       "| fulvestrant | -0.281245 | 0.009065718 |\n",
-       "| phenazopyridine | -0.321425 | 0.009136916 |\n",
-       "| ... | ... | ... |\n",
-       "| PF-00562151-00 | 0 | 1 |\n",
-       "| pioglitazone | 0 | 1 |\n",
-       "| PF-00539745-00 | 0 | 1 |\n",
-       "| valdecoxib | 0 | 1 |\n",
-       "| PF-00539758-00 | 0 | 1 |\n",
-       "| orlistat | 0 | 1 |\n",
-       "| 5707885 | 0 | 1 |\n",
-       "| C-75 | 0 | 1 |\n",
-       "| 5155877 | 0 | 1 |\n",
-       "| dinoprostone | 0 | 1 |\n",
-       "| 5194442 | 0 | 1 |\n",
-       "| AG-028671 | 0 | 1 |\n",
-       "| 6-bromoindirubin-3'-oxime | 0 | 1 |\n",
-       "| Gly-His-Lys | 0 | 1 |\n",
-       "| STOCK1N-35696 | 0 | 1 |\n",
-       "| STOCK1N-28457 | 0 | 1 |\n",
-       "| H-89 | 0 | 1 |\n",
-       "| SB-202190 | 0 | 1 |\n",
-       "| NS-398 | 0 | 1 |\n",
-       "| SB-203580 | 0 | 1 |\n",
-       "| AH-6809 | 0 | 1 |\n",
-       "| alsterpaullone | 0 | 1 |\n",
-       "| SC-19220 | 0 | 1 |\n",
-       "| 0198306-0000 | 0 | 1 |\n",
-       "| AR-A014418 | 0 | 1 |\n",
-       "| semustine | 0 | 1 |\n",
-       "| CP-944629 | 0 | 1 |\n",
-       "| irinotecan | 0 | 1 |\n",
-       "| BCB000039 | 0 | 1 |\n",
-       "| 11-deoxy-16,16-dimethylprostaglandin E2 | 0 | 1 |\n",
-       "\n"
-      ],
-      "text/plain": [
-       "                                        Connectivity P_value    \n",
-       "valproic acid                           -0.376625    0.003243431\n",
-       "rifabutin                               -0.340380    0.003249652\n",
-       "levomepromazine                         -0.329905    0.003363063\n",
-       "promazine                               -0.338460    0.003408985\n",
-       "Prestwick-559                           -0.332285    0.003453743\n",
-       "maprotiline                             -0.345995    0.003483930\n",
-       "nicergoline                             -0.297975    0.003540995\n",
-       "GW-8510                                 -0.365775    0.003643482\n",
-       "lasalocid                               -0.287965    0.003653011\n",
-       "pyrvinium                               -0.312920    0.003692544\n",
-       "nortriptyline                           -0.346990    0.003785772\n",
-       "prochlorperazine                        -0.360245    0.003809080\n",
-       "norcyclobenzaprine                      -0.319960    0.003935323\n",
-       "fluphenazine                            -0.351740    0.004089757\n",
-       "LY-294002                               -0.358135    0.004118938\n",
-       "raloxifene                              -0.301795    0.004218595\n",
-       "4,5-dianilinophthalimide                -0.809330    0.006282675\n",
-       "trichostatin A                          -0.330245    0.006335983\n",
-       "eucatropine                             -0.288555    0.006421429\n",
-       "syrosingopine                           -0.318895    0.006459413\n",
-       "mebendazole                             -0.300325    0.006618701\n",
-       "lycorine                                 0.319895    0.006644780\n",
-       "rescinnamine                            -0.323295    0.006987249\n",
-       "reserpine                               -0.285080    0.007184183\n",
-       "sirolimus                               -0.361685    0.007393165\n",
-       "trifluoperazine                         -0.375195    0.007405285\n",
-       "vorinostat                              -0.378310    0.008683363\n",
-       "methotrexate                            -0.336405    0.008864197\n",
-       "fulvestrant                             -0.281245    0.009065718\n",
-       "phenazopyridine                         -0.321425    0.009136916\n",
-       "...                                     ...          ...        \n",
-       "PF-00562151-00                          0            1          \n",
-       "pioglitazone                            0            1          \n",
-       "PF-00539745-00                          0            1          \n",
-       "valdecoxib                              0            1          \n",
-       "PF-00539758-00                          0            1          \n",
-       "orlistat                                0            1          \n",
-       "5707885                                 0            1          \n",
-       "C-75                                    0            1          \n",
-       "5155877                                 0            1          \n",
-       "dinoprostone                            0            1          \n",
-       "5194442                                 0            1          \n",
-       "AG-028671                               0            1          \n",
-       "6-bromoindirubin-3'-oxime               0            1          \n",
-       "Gly-His-Lys                             0            1          \n",
-       "STOCK1N-35696                           0            1          \n",
-       "STOCK1N-28457                           0            1          \n",
-       "H-89                                    0            1          \n",
-       "SB-202190                               0            1          \n",
-       "NS-398                                  0            1          \n",
-       "SB-203580                               0            1          \n",
-       "AH-6809                                 0            1          \n",
-       "alsterpaullone                          0            1          \n",
-       "SC-19220                                0            1          \n",
-       "0198306-0000                            0            1          \n",
-       "AR-A014418                              0            1          \n",
-       "semustine                               0            1          \n",
-       "CP-944629                               0            1          \n",
-       "irinotecan                              0            1          \n",
-       "BCB000039                               0            1          \n",
-       "11-deoxy-16,16-dimethylprostaglandin E2 0            1          "
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "p_value_sars\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 87,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "mers_up_and_down_genes <-read.csv(\"HCoV_EMC2012_24Hour_23631916_GSE45042.csv\",stringsAsFactors = F, header = T, sep=\";\")\n",
-    "rownames(mers_up_and_down_genes) <- mers_up_and_down_genes$Feature\n",
-    "mers<- mers_up_and_down_genes$Direction\n",
-    "names(mers) <- rownames(mers_up_and_down_genes)\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 88,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "res_mers <- apply(drug.perturbation[,,c(\"tstat\", \"fdr\")], \n",
-    "             2,function(x, mers){\n",
-    "         return(connectivityScore(x=x, \n",
-    "                                  y=mers,\n",
-    "                               method=\"fgsea\", nperm=100))\n",
-    "       },mers = mers)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 89,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "rownames(res_mers) <- c(\"Connectivity\", \"P_value\")\n",
-    "res_mers <- t(res_mers)\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 98,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "con_score <-res_mers[order((res_mers[,1]),decreasing = F),]\n",
-    "p_value <- res_mers[order((res_mers[,2]),decreasing = F),]\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 99,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<table>\n",
-       "<caption>A matrix: 1288 × 2 of type dbl</caption>\n",
-       "<thead>\n",
-       "\t<tr><th></th><th scope=col>Connectivity</th><th scope=col>P_value</th></tr>\n",
-       "</thead>\n",
-       "<tbody>\n",
-       "\t<tr><th scope=row>valproic acid</th><td>-0.376625</td><td>0.003319676</td></tr>\n",
-       "\t<tr><th scope=row>flupentixol</th><td>-0.269090</td><td>0.003383565</td></tr>\n",
-       "\t<tr><th scope=row>syrosingopine</th><td>-0.318895</td><td>0.003397262</td></tr>\n",
-       "\t<tr><th scope=row>levomepromazine</th><td>-0.329905</td><td>0.003426580</td></tr>\n",
-       "\t<tr><th scope=row>eucatropine</th><td>-0.288555</td><td>0.003468201</td></tr>\n",
-       "\t<tr><th scope=row>vorinostat</th><td>-0.378310</td><td>0.003530871</td></tr>\n",
-       "\t<tr><th scope=row>prochlorperazine</th><td>-0.360245</td><td>0.003554838</td></tr>\n",
-       "\t<tr><th scope=row>rescinnamine</th><td>-0.323295</td><td>0.003575237</td></tr>\n",
-       "\t<tr><th scope=row>maprotiline</th><td>-0.345995</td><td>0.003584323</td></tr>\n",
-       "\t<tr><th scope=row>promazine</th><td>-0.338460</td><td>0.003632854</td></tr>\n",
-       "\t<tr><th scope=row>phenazopyridine</th><td>-0.321425</td><td>0.003734297</td></tr>\n",
-       "\t<tr><th scope=row>nortriptyline</th><td>-0.346990</td><td>0.003890230</td></tr>\n",
-       "\t<tr><th scope=row>norcyclobenzaprine</th><td>-0.319960</td><td>0.003968853</td></tr>\n",
-       "\t<tr><th scope=row>lasalocid</th><td>-0.287965</td><td>0.004218595</td></tr>\n",
-       "\t<tr><th scope=row>trifluoperazine</th><td>-0.375195</td><td>0.004504136</td></tr>\n",
-       "\t<tr><th scope=row>fluphenazine</th><td>-0.351740</td><td>0.004867912</td></tr>\n",
-       "\t<tr><th scope=row>sirolimus</th><td>-0.361685</td><td>0.005503567</td></tr>\n",
-       "\t<tr><th scope=row>methotrexate</th><td>-0.336405</td><td>0.006284774</td></tr>\n",
-       "\t<tr><th scope=row>resveratrol</th><td>-0.350465</td><td>0.006437040</td></tr>\n",
-       "\t<tr><th scope=row>nicergoline</th><td>-0.297975</td><td>0.006459316</td></tr>\n",
-       "\t<tr><th scope=row>GW-8510</th><td>-0.365775</td><td>0.006644780</td></tr>\n",
-       "\t<tr><th scope=row>LY-294002</th><td>-0.358135</td><td>0.006971206</td></tr>\n",
-       "\t<tr><th scope=row>antimycin A</th><td>-0.282915</td><td>0.006971206</td></tr>\n",
-       "\t<tr><th scope=row>chlorpromazine</th><td>-0.312550</td><td>0.006971420</td></tr>\n",
-       "\t<tr><th scope=row>ampyrone</th><td>-0.302000</td><td>0.007577828</td></tr>\n",
-       "\t<tr><th scope=row>trichostatin A</th><td>-0.330245</td><td>0.008959310</td></tr>\n",
-       "\t<tr><th scope=row>bromocriptine</th><td>-0.298380</td><td>0.009140214</td></tr>\n",
-       "\t<tr><th scope=row>cefadroxil</th><td>-0.302460</td><td>0.009152568</td></tr>\n",
-       "\t<tr><th scope=row>HC toxin</th><td>-0.371125</td><td>0.009495673</td></tr>\n",
-       "\t<tr><th scope=row>fluspirilene</th><td>-0.271445</td><td>0.009801250</td></tr>\n",
-       "\t<tr><th scope=row>...</th><td>...</td><td>...</td></tr>\n",
-       "\t<tr><th scope=row>PF-00562151-00</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>pioglitazone</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>PF-00539745-00</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>valdecoxib</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>PF-00539758-00</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>orlistat</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>5707885</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>C-75</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>5155877</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>dinoprostone</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>5194442</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>AG-028671</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>6-bromoindirubin-3'-oxime</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>Gly-His-Lys</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>STOCK1N-35696</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>STOCK1N-28457</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>H-89</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>SB-202190</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>NS-398</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>SB-203580</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>AH-6809</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>alsterpaullone</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>SC-19220</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>0198306-0000</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>AR-A014418</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>semustine</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>CP-944629</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>irinotecan</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>BCB000039</th><td>0</td><td>1</td></tr>\n",
-       "\t<tr><th scope=row>11-deoxy-16,16-dimethylprostaglandin E2</th><td>0</td><td>1</td></tr>\n",
-       "</tbody>\n",
-       "</table>\n"
-      ],
-      "text/latex": [
-       "A matrix: 1288 × 2 of type dbl\n",
-       "\\begin{tabular}{r|ll}\n",
-       "  & Connectivity & P\\_value\\\\\n",
-       "\\hline\n",
-       "\tvalproic acid & -0.376625 & 0.003319676\\\\\n",
-       "\tflupentixol & -0.269090 & 0.003383565\\\\\n",
-       "\tsyrosingopine & -0.318895 & 0.003397262\\\\\n",
-       "\tlevomepromazine & -0.329905 & 0.003426580\\\\\n",
-       "\teucatropine & -0.288555 & 0.003468201\\\\\n",
-       "\tvorinostat & -0.378310 & 0.003530871\\\\\n",
-       "\tprochlorperazine & -0.360245 & 0.003554838\\\\\n",
-       "\trescinnamine & -0.323295 & 0.003575237\\\\\n",
-       "\tmaprotiline & -0.345995 & 0.003584323\\\\\n",
-       "\tpromazine & -0.338460 & 0.003632854\\\\\n",
-       "\tphenazopyridine & -0.321425 & 0.003734297\\\\\n",
-       "\tnortriptyline & -0.346990 & 0.003890230\\\\\n",
-       "\tnorcyclobenzaprine & -0.319960 & 0.003968853\\\\\n",
-       "\tlasalocid & -0.287965 & 0.004218595\\\\\n",
-       "\ttrifluoperazine & -0.375195 & 0.004504136\\\\\n",
-       "\tfluphenazine & -0.351740 & 0.004867912\\\\\n",
-       "\tsirolimus & -0.361685 & 0.005503567\\\\\n",
-       "\tmethotrexate & -0.336405 & 0.006284774\\\\\n",
-       "\tresveratrol & -0.350465 & 0.006437040\\\\\n",
-       "\tnicergoline & -0.297975 & 0.006459316\\\\\n",
-       "\tGW-8510 & -0.365775 & 0.006644780\\\\\n",
-       "\tLY-294002 & -0.358135 & 0.006971206\\\\\n",
-       "\tantimycin A & -0.282915 & 0.006971206\\\\\n",
-       "\tchlorpromazine & -0.312550 & 0.006971420\\\\\n",
-       "\tampyrone & -0.302000 & 0.007577828\\\\\n",
-       "\ttrichostatin A & -0.330245 & 0.008959310\\\\\n",
-       "\tbromocriptine & -0.298380 & 0.009140214\\\\\n",
-       "\tcefadroxil & -0.302460 & 0.009152568\\\\\n",
-       "\tHC toxin & -0.371125 & 0.009495673\\\\\n",
-       "\tfluspirilene & -0.271445 & 0.009801250\\\\\n",
-       "\t... & ... & ...\\\\\n",
-       "\tPF-00562151-00 & 0 & 1\\\\\n",
-       "\tpioglitazone & 0 & 1\\\\\n",
-       "\tPF-00539745-00 & 0 & 1\\\\\n",
-       "\tvaldecoxib & 0 & 1\\\\\n",
-       "\tPF-00539758-00 & 0 & 1\\\\\n",
-       "\torlistat & 0 & 1\\\\\n",
-       "\t5707885 & 0 & 1\\\\\n",
-       "\tC-75 & 0 & 1\\\\\n",
-       "\t5155877 & 0 & 1\\\\\n",
-       "\tdinoprostone & 0 & 1\\\\\n",
-       "\t5194442 & 0 & 1\\\\\n",
-       "\tAG-028671 & 0 & 1\\\\\n",
-       "\t6-bromoindirubin-3'-oxime & 0 & 1\\\\\n",
-       "\tGly-His-Lys & 0 & 1\\\\\n",
-       "\tSTOCK1N-35696 & 0 & 1\\\\\n",
-       "\tSTOCK1N-28457 & 0 & 1\\\\\n",
-       "\tH-89 & 0 & 1\\\\\n",
-       "\tSB-202190 & 0 & 1\\\\\n",
-       "\tNS-398 & 0 & 1\\\\\n",
-       "\tSB-203580 & 0 & 1\\\\\n",
-       "\tAH-6809 & 0 & 1\\\\\n",
-       "\talsterpaullone & 0 & 1\\\\\n",
-       "\tSC-19220 & 0 & 1\\\\\n",
-       "\t0198306-0000 & 0 & 1\\\\\n",
-       "\tAR-A014418 & 0 & 1\\\\\n",
-       "\tsemustine & 0 & 1\\\\\n",
-       "\tCP-944629 & 0 & 1\\\\\n",
-       "\tirinotecan & 0 & 1\\\\\n",
-       "\tBCB000039 & 0 & 1\\\\\n",
-       "\t11-deoxy-16,16-dimethylprostaglandin E2 & 0 & 1\\\\\n",
-       "\\end{tabular}\n"
-      ],
-      "text/markdown": [
-       "\n",
-       "A matrix: 1288 × 2 of type dbl\n",
-       "\n",
-       "| <!--/--> | Connectivity | P_value |\n",
-       "|---|---|---|\n",
-       "| valproic acid | -0.376625 | 0.003319676 |\n",
-       "| flupentixol | -0.269090 | 0.003383565 |\n",
-       "| syrosingopine | -0.318895 | 0.003397262 |\n",
-       "| levomepromazine | -0.329905 | 0.003426580 |\n",
-       "| eucatropine | -0.288555 | 0.003468201 |\n",
-       "| vorinostat | -0.378310 | 0.003530871 |\n",
-       "| prochlorperazine | -0.360245 | 0.003554838 |\n",
-       "| rescinnamine | -0.323295 | 0.003575237 |\n",
-       "| maprotiline | -0.345995 | 0.003584323 |\n",
-       "| promazine | -0.338460 | 0.003632854 |\n",
-       "| phenazopyridine | -0.321425 | 0.003734297 |\n",
-       "| nortriptyline | -0.346990 | 0.003890230 |\n",
-       "| norcyclobenzaprine | -0.319960 | 0.003968853 |\n",
-       "| lasalocid | -0.287965 | 0.004218595 |\n",
-       "| trifluoperazine | -0.375195 | 0.004504136 |\n",
-       "| fluphenazine | -0.351740 | 0.004867912 |\n",
-       "| sirolimus | -0.361685 | 0.005503567 |\n",
-       "| methotrexate | -0.336405 | 0.006284774 |\n",
-       "| resveratrol | -0.350465 | 0.006437040 |\n",
-       "| nicergoline | -0.297975 | 0.006459316 |\n",
-       "| GW-8510 | -0.365775 | 0.006644780 |\n",
-       "| LY-294002 | -0.358135 | 0.006971206 |\n",
-       "| antimycin A | -0.282915 | 0.006971206 |\n",
-       "| chlorpromazine | -0.312550 | 0.006971420 |\n",
-       "| ampyrone | -0.302000 | 0.007577828 |\n",
-       "| trichostatin A | -0.330245 | 0.008959310 |\n",
-       "| bromocriptine | -0.298380 | 0.009140214 |\n",
-       "| cefadroxil | -0.302460 | 0.009152568 |\n",
-       "| HC toxin | -0.371125 | 0.009495673 |\n",
-       "| fluspirilene | -0.271445 | 0.009801250 |\n",
-       "| ... | ... | ... |\n",
-       "| PF-00562151-00 | 0 | 1 |\n",
-       "| pioglitazone | 0 | 1 |\n",
-       "| PF-00539745-00 | 0 | 1 |\n",
-       "| valdecoxib | 0 | 1 |\n",
-       "| PF-00539758-00 | 0 | 1 |\n",
-       "| orlistat | 0 | 1 |\n",
-       "| 5707885 | 0 | 1 |\n",
-       "| C-75 | 0 | 1 |\n",
-       "| 5155877 | 0 | 1 |\n",
-       "| dinoprostone | 0 | 1 |\n",
-       "| 5194442 | 0 | 1 |\n",
-       "| AG-028671 | 0 | 1 |\n",
-       "| 6-bromoindirubin-3'-oxime | 0 | 1 |\n",
-       "| Gly-His-Lys | 0 | 1 |\n",
-       "| STOCK1N-35696 | 0 | 1 |\n",
-       "| STOCK1N-28457 | 0 | 1 |\n",
-       "| H-89 | 0 | 1 |\n",
-       "| SB-202190 | 0 | 1 |\n",
-       "| NS-398 | 0 | 1 |\n",
-       "| SB-203580 | 0 | 1 |\n",
-       "| AH-6809 | 0 | 1 |\n",
-       "| alsterpaullone | 0 | 1 |\n",
-       "| SC-19220 | 0 | 1 |\n",
-       "| 0198306-0000 | 0 | 1 |\n",
-       "| AR-A014418 | 0 | 1 |\n",
-       "| semustine | 0 | 1 |\n",
-       "| CP-944629 | 0 | 1 |\n",
-       "| irinotecan | 0 | 1 |\n",
-       "| BCB000039 | 0 | 1 |\n",
-       "| 11-deoxy-16,16-dimethylprostaglandin E2 | 0 | 1 |\n",
-       "\n"
-      ],
-      "text/plain": [
-       "                                        Connectivity P_value    \n",
-       "valproic acid                           -0.376625    0.003319676\n",
-       "flupentixol                             -0.269090    0.003383565\n",
-       "syrosingopine                           -0.318895    0.003397262\n",
-       "levomepromazine                         -0.329905    0.003426580\n",
-       "eucatropine                             -0.288555    0.003468201\n",
-       "vorinostat                              -0.378310    0.003530871\n",
-       "prochlorperazine                        -0.360245    0.003554838\n",
-       "rescinnamine                            -0.323295    0.003575237\n",
-       "maprotiline                             -0.345995    0.003584323\n",
-       "promazine                               -0.338460    0.003632854\n",
-       "phenazopyridine                         -0.321425    0.003734297\n",
-       "nortriptyline                           -0.346990    0.003890230\n",
-       "norcyclobenzaprine                      -0.319960    0.003968853\n",
-       "lasalocid                               -0.287965    0.004218595\n",
-       "trifluoperazine                         -0.375195    0.004504136\n",
-       "fluphenazine                            -0.351740    0.004867912\n",
-       "sirolimus                               -0.361685    0.005503567\n",
-       "methotrexate                            -0.336405    0.006284774\n",
-       "resveratrol                             -0.350465    0.006437040\n",
-       "nicergoline                             -0.297975    0.006459316\n",
-       "GW-8510                                 -0.365775    0.006644780\n",
-       "LY-294002                               -0.358135    0.006971206\n",
-       "antimycin A                             -0.282915    0.006971206\n",
-       "chlorpromazine                          -0.312550    0.006971420\n",
-       "ampyrone                                -0.302000    0.007577828\n",
-       "trichostatin A                          -0.330245    0.008959310\n",
-       "bromocriptine                           -0.298380    0.009140214\n",
-       "cefadroxil                              -0.302460    0.009152568\n",
-       "HC toxin                                -0.371125    0.009495673\n",
-       "fluspirilene                            -0.271445    0.009801250\n",
-       "...                                     ...          ...        \n",
-       "PF-00562151-00                          0            1          \n",
-       "pioglitazone                            0            1          \n",
-       "PF-00539745-00                          0            1          \n",
-       "valdecoxib                              0            1          \n",
-       "PF-00539758-00                          0            1          \n",
-       "orlistat                                0            1          \n",
-       "5707885                                 0            1          \n",
-       "C-75                                    0            1          \n",
-       "5155877                                 0            1          \n",
-       "dinoprostone                            0            1          \n",
-       "5194442                                 0            1          \n",
-       "AG-028671                               0            1          \n",
-       "6-bromoindirubin-3'-oxime               0            1          \n",
-       "Gly-His-Lys                             0            1          \n",
-       "STOCK1N-35696                           0            1          \n",
-       "STOCK1N-28457                           0            1          \n",
-       "H-89                                    0            1          \n",
-       "SB-202190                               0            1          \n",
-       "NS-398                                  0            1          \n",
-       "SB-203580                               0            1          \n",
-       "AH-6809                                 0            1          \n",
-       "alsterpaullone                          0            1          \n",
-       "SC-19220                                0            1          \n",
-       "0198306-0000                            0            1          \n",
-       "AR-A014418                              0            1          \n",
-       "semustine                               0            1          \n",
-       "CP-944629                               0            1          \n",
-       "irinotecan                              0            1          \n",
-       "BCB000039                               0            1          \n",
-       "11-deoxy-16,16-dimethylprostaglandin E2 0            1          "
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "p_value"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 92,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "write.csv(p_value,\"mers_results.csv\", row.names = T)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 93,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "write.csv(p_value_sars,\"sars_results.csv\", row.names = T)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Based on p value and connectivity score (negative score means that drug reverses the disease signature) I have decided to do \n",
-    "docking on valproic acid. This drug is FDA-approved for treatment of epilepsy, bipolar disorder  and migraine headeche. \n",
-    "Valproic acid is also tested in the treatment of AIDS and cancer.\n",
-    "I also in my results get that sirolimus can be used against coronaviruses, and study by Zhou et al get the similar results.\n",
-    " \n",
-    "References:\n",
-    "Yadi Zhou, Yuan Hou, Jiayu Shen, Yin Huang, William Martin, Feixiong Cheng.Network-based Drug Repurposing for Human Coronavirus\n",
-    "doi: https://doi.org/10.1101/2020.02.03.20020263\n",
-    "\n",
-    "O. Trott, A. J. Olson,AutoDock Vina: improving the speed and accuracy of dockingwith a new scoring function,\n",
-    "efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010); 455-461; DOI 10.1002/jcc.21334  \n",
-    "\n",
-    "Study of Valproic Acid to Treat HIV Infected Adults https://clinicaltrials.gov/ct2/show/NCT00312546\n",
-    "\n",
-    "Vázquez-Calvo A, Saiz JC, Sobrino F, Martín-Acebes MA. Inhibition of enveloped virus infection of cultured cells by valproic acid.\n",
-    "J Virol. 2011;85(3):1267–1274. doi:10.1128/JVI.01717-10"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "R",
-   "language": "R",
-   "name": "ir"
-  },
-  "language_info": {
-   "codemirror_mode": "r",
-   "file_extension": ".r",
-   "mimetype": "text/x-r-source",
-   "name": "R",
-   "pygments_lexer": "r",
-   "version": "3.6.1"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 2
-}