notebooks/03_exp_matrix_4ESTIMATE.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {
    "toc": true
   },
   "source": [
    "<h1>Table of Contents<span class=\"tocSkip\"></span></h1>\n",
    "<div class=\"toc\"><ul class=\"toc-item\"><li><span><a href=\"#Dependencies\" data-toc-modified-id=\"Dependencies-1\">Dependencies</a></span></li><li><span><a href=\"#Functions\" data-toc-modified-id=\"Functions-2\">Functions</a></span></li><li><span><a href=\"#Paths\" data-toc-modified-id=\"Paths-3\">Paths</a></span></li><li><span><a href=\"#Main\" data-toc-modified-id=\"Main-4\">Main</a></span><ul class=\"toc-item\"><li><span><a href=\"#CBTTC\" data-toc-modified-id=\"CBTTC-4.1\">CBTTC</a></span></li></ul></li></ul></div>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Dependencies"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "library(tidyr)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Functions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "matchexp_matrixfx <- function(exp_matrix, estimate_manifest, group, sample_type, matchingcol){\n",
    "    \n",
    "    message(\"dimensions of exp_matrix: \", deparse(substitute(exp_matrix)))\n",
    "    print(dim(exp_matrix))\n",
    "    \n",
    "    subset_estimate_manifest <- estimate_manifest[estimate_manifest$group == group,]\n",
    "    subset_estimate_manifest_sampletype <- subset_estimate_manifest[grepl(sample_type,\n",
    "                                                                    subset_estimate_manifest$sample_type),]\n",
    "    \n",
    "    message(\"dimensions of estimate_manifest_df for: \", group, \" sample_type:\", sample_type)\n",
    "    print(dim(subset_estimate_manifest_sampletype))\n",
    "    \n",
    "    exp_matrix_matchingset <- exp_matrix[,colnames(exp_matrix) %in% \n",
    "                                         subset_estimate_manifest_sampletype[[matchingcol]]]\n",
    "    \n",
    "    message(\"dimensions of exp_matrix_matchingset for: \", deparse(substitute(exp_matrix)), \n",
    "            \" with matching column: \", matchingcol)\n",
    "    print(dim(exp_matrix_matchingset))\n",
    "    \n",
    "    exp_matrix_matchingset <- cbind(exp_matrix[,1:2], exp_matrix_matchingset)\n",
    "\n",
    "    return(exp_matrix_matchingset)\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "longtowidefx <- function(long_exp_matrix){ \n",
    "    wide_exp_matrix <- spread(long_exp_matrix, key = \"sample\", value = \"tpm\")\n",
    "    return(wide_exp_matrix)\n",
    "}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Paths"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "manifestpath <- \"/Users/anabbi/OneDrive - UHN/Documents/IPD2/Manifests/\"\n",
    "datapath <- \"/Users/anabbi/OneDrive - UHN/Documents/IPD2/Data/\"\n",
    "plotpath <- \"/Users/anabbi/OneDrive - UHN/Documents/IPD2/Plots/\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Main"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## CBTTC"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "From Cavatica"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "CBTTCtpm <- read.table(paste0(datapath, \"exp_mat/KF_CBTTC_tpm_rsem_matrix.txt_sampleid.txt\"), sep = \"\\t\",\n",
    "                    header = TRUE, stringsAsFactors = FALSE, check.names = F)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table class=\"dataframe\">\n",
       "<caption>A data.frame: 6 × 970</caption>\n",
       "<thead>\n",
       "\t<tr><th></th><th scope=col></th><th scope=col>7316-2599</th><th scope=col>7316-1926</th><th scope=col>7316-489</th><th scope=col>7316-16</th><th scope=col>7316-13</th><th scope=col>7316-3936</th><th scope=col>7316-3632</th><th scope=col>7316-873</th><th scope=col>7316-2669</th><th scope=col>⋯</th><th scope=col>7316-2589</th><th scope=col>7316-395</th><th scope=col>7316-1785</th><th scope=col>7316-2744</th><th scope=col>7316-1116</th><th scope=col>7316-333</th><th scope=col>7316-775</th><th scope=col>7316-96</th><th scope=col>7316-1750</th><th scope=col>7316-3963</th></tr>\n",
       "\t<tr><th></th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>⋯</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>1</th><td>ENSG00000000003.14_TSPAN6  </td><td>10.99</td><td>8.66</td><td>6.15</td><td>2.40</td><td>0.73</td><td>1.50</td><td>1.88</td><td>29.41</td><td>4.62</td><td>⋯</td><td>2.36</td><td>2.76</td><td>12.78</td><td>11.24</td><td>7.41</td><td>29.74</td><td>3.04</td><td>5.81</td><td>2.59</td><td>1.38</td></tr>\n",
       "\t<tr><th scope=row>2</th><td>ENSG00000000005.5_TNMD     </td><td> 0.18</td><td>0.02</td><td>0.03</td><td>0.02</td><td>0.02</td><td>0.01</td><td>0.03</td><td> 0.33</td><td>0.03</td><td>⋯</td><td>0.00</td><td>0.02</td><td> 0.01</td><td> 0.53</td><td>0.01</td><td> 0.02</td><td>0.00</td><td>0.01</td><td>0.01</td><td>0.00</td></tr>\n",
       "\t<tr><th scope=row>3</th><td>ENSG00000000419.12_DPM1    </td><td> 4.95</td><td>6.15</td><td>5.09</td><td>3.35</td><td>1.09</td><td>3.68</td><td>3.27</td><td> 4.89</td><td>4.75</td><td>⋯</td><td>2.26</td><td>2.37</td><td> 8.97</td><td> 4.07</td><td>8.08</td><td>29.66</td><td>2.58</td><td>7.43</td><td>3.14</td><td>2.83</td></tr>\n",
       "\t<tr><th scope=row>4</th><td>ENSG00000000457.13_SCYL3   </td><td> 1.50</td><td>1.75</td><td>1.71</td><td>0.90</td><td>0.44</td><td>1.44</td><td>0.89</td><td> 1.52</td><td>1.61</td><td>⋯</td><td>0.65</td><td>0.68</td><td> 1.43</td><td> 1.38</td><td>2.05</td><td> 9.99</td><td>1.52</td><td>2.62</td><td>1.40</td><td>0.71</td></tr>\n",
       "\t<tr><th scope=row>5</th><td>ENSG00000000460.16_C1orf112</td><td> 1.70</td><td>1.12</td><td>2.78</td><td>0.34</td><td>0.43</td><td>0.71</td><td>0.57</td><td> 1.00</td><td>1.64</td><td>⋯</td><td>0.45</td><td>0.50</td><td> 4.22</td><td> 0.71</td><td>0.98</td><td> 7.38</td><td>0.82</td><td>1.69</td><td>1.08</td><td>0.65</td></tr>\n",
       "\t<tr><th scope=row>6</th><td>ENSG00000000938.12_FGR     </td><td> 1.27</td><td>0.90</td><td>0.18</td><td>1.12</td><td>0.36</td><td>1.32</td><td>1.05</td><td> 0.93</td><td>1.01</td><td>⋯</td><td>0.36</td><td>3.15</td><td> 3.78</td><td> 0.44</td><td>1.51</td><td> 2.06</td><td>0.19</td><td>0.53</td><td>1.54</td><td>5.57</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.frame: 6 × 970\n",
       "\\begin{tabular}{r|lllllllllllllllllllll}\n",
       "  &  & 7316-2599 & 7316-1926 & 7316-489 & 7316-16 & 7316-13 & 7316-3936 & 7316-3632 & 7316-873 & 7316-2669 & ⋯ & 7316-2589 & 7316-395 & 7316-1785 & 7316-2744 & 7316-1116 & 7316-333 & 7316-775 & 7316-96 & 7316-1750 & 7316-3963\\\\\n",
       "  & <chr> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & ⋯ & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl>\\\\\n",
       "\\hline\n",
       "\t1 & ENSG00000000003.14\\_TSPAN6   & 10.99 & 8.66 & 6.15 & 2.40 & 0.73 & 1.50 & 1.88 & 29.41 & 4.62 & ⋯ & 2.36 & 2.76 & 12.78 & 11.24 & 7.41 & 29.74 & 3.04 & 5.81 & 2.59 & 1.38\\\\\n",
       "\t2 & ENSG00000000005.5\\_TNMD      &  0.18 & 0.02 & 0.03 & 0.02 & 0.02 & 0.01 & 0.03 &  0.33 & 0.03 & ⋯ & 0.00 & 0.02 &  0.01 &  0.53 & 0.01 &  0.02 & 0.00 & 0.01 & 0.01 & 0.00\\\\\n",
       "\t3 & ENSG00000000419.12\\_DPM1     &  4.95 & 6.15 & 5.09 & 3.35 & 1.09 & 3.68 & 3.27 &  4.89 & 4.75 & ⋯ & 2.26 & 2.37 &  8.97 &  4.07 & 8.08 & 29.66 & 2.58 & 7.43 & 3.14 & 2.83\\\\\n",
       "\t4 & ENSG00000000457.13\\_SCYL3    &  1.50 & 1.75 & 1.71 & 0.90 & 0.44 & 1.44 & 0.89 &  1.52 & 1.61 & ⋯ & 0.65 & 0.68 &  1.43 &  1.38 & 2.05 &  9.99 & 1.52 & 2.62 & 1.40 & 0.71\\\\\n",
       "\t5 & ENSG00000000460.16\\_C1orf112 &  1.70 & 1.12 & 2.78 & 0.34 & 0.43 & 0.71 & 0.57 &  1.00 & 1.64 & ⋯ & 0.45 & 0.50 &  4.22 &  0.71 & 0.98 &  7.38 & 0.82 & 1.69 & 1.08 & 0.65\\\\\n",
       "\t6 & ENSG00000000938.12\\_FGR      &  1.27 & 0.90 & 0.18 & 1.12 & 0.36 & 1.32 & 1.05 &  0.93 & 1.01 & ⋯ & 0.36 & 3.15 &  3.78 &  0.44 & 1.51 &  2.06 & 0.19 & 0.53 & 1.54 & 5.57\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.frame: 6 × 970\n",
       "\n",
       "| <!--/--> | <!----> &lt;chr&gt; | 7316-2599 &lt;dbl&gt; | 7316-1926 &lt;dbl&gt; | 7316-489 &lt;dbl&gt; | 7316-16 &lt;dbl&gt; | 7316-13 &lt;dbl&gt; | 7316-3936 &lt;dbl&gt; | 7316-3632 &lt;dbl&gt; | 7316-873 &lt;dbl&gt; | 7316-2669 &lt;dbl&gt; | ⋯ ⋯ | 7316-2589 &lt;dbl&gt; | 7316-395 &lt;dbl&gt; | 7316-1785 &lt;dbl&gt; | 7316-2744 &lt;dbl&gt; | 7316-1116 &lt;dbl&gt; | 7316-333 &lt;dbl&gt; | 7316-775 &lt;dbl&gt; | 7316-96 &lt;dbl&gt; | 7316-1750 &lt;dbl&gt; | 7316-3963 &lt;dbl&gt; |\n",
       "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
       "| 1 | ENSG00000000003.14_TSPAN6   | 10.99 | 8.66 | 6.15 | 2.40 | 0.73 | 1.50 | 1.88 | 29.41 | 4.62 | ⋯ | 2.36 | 2.76 | 12.78 | 11.24 | 7.41 | 29.74 | 3.04 | 5.81 | 2.59 | 1.38 |\n",
       "| 2 | ENSG00000000005.5_TNMD      |  0.18 | 0.02 | 0.03 | 0.02 | 0.02 | 0.01 | 0.03 |  0.33 | 0.03 | ⋯ | 0.00 | 0.02 |  0.01 |  0.53 | 0.01 |  0.02 | 0.00 | 0.01 | 0.01 | 0.00 |\n",
       "| 3 | ENSG00000000419.12_DPM1     |  4.95 | 6.15 | 5.09 | 3.35 | 1.09 | 3.68 | 3.27 |  4.89 | 4.75 | ⋯ | 2.26 | 2.37 |  8.97 |  4.07 | 8.08 | 29.66 | 2.58 | 7.43 | 3.14 | 2.83 |\n",
       "| 4 | ENSG00000000457.13_SCYL3    |  1.50 | 1.75 | 1.71 | 0.90 | 0.44 | 1.44 | 0.89 |  1.52 | 1.61 | ⋯ | 0.65 | 0.68 |  1.43 |  1.38 | 2.05 |  9.99 | 1.52 | 2.62 | 1.40 | 0.71 |\n",
       "| 5 | ENSG00000000460.16_C1orf112 |  1.70 | 1.12 | 2.78 | 0.34 | 0.43 | 0.71 | 0.57 |  1.00 | 1.64 | ⋯ | 0.45 | 0.50 |  4.22 |  0.71 | 0.98 |  7.38 | 0.82 | 1.69 | 1.08 | 0.65 |\n",
       "| 6 | ENSG00000000938.12_FGR      |  1.27 | 0.90 | 0.18 | 1.12 | 0.36 | 1.32 | 1.05 |  0.93 | 1.01 | ⋯ | 0.36 | 3.15 |  3.78 |  0.44 | 1.51 |  2.06 | 0.19 | 0.53 | 1.54 | 5.57 |\n",
       "\n"
      ],
      "text/plain": [
       "                              7316-2599 7316-1926 7316-489 7316-16 7316-13\n",
       "1 ENSG00000000003.14_TSPAN6   10.99     8.66      6.15     2.40    0.73   \n",
       "2 ENSG00000000005.5_TNMD       0.18     0.02      0.03     0.02    0.02   \n",
       "3 ENSG00000000419.12_DPM1      4.95     6.15      5.09     3.35    1.09   \n",
       "4 ENSG00000000457.13_SCYL3     1.50     1.75      1.71     0.90    0.44   \n",
       "5 ENSG00000000460.16_C1orf112  1.70     1.12      2.78     0.34    0.43   \n",
       "6 ENSG00000000938.12_FGR       1.27     0.90      0.18     1.12    0.36   \n",
       "  7316-3936 7316-3632 7316-873 7316-2669 ⋯ 7316-2589 7316-395 7316-1785\n",
       "1 1.50      1.88      29.41    4.62      ⋯ 2.36      2.76     12.78    \n",
       "2 0.01      0.03       0.33    0.03      ⋯ 0.00      0.02      0.01    \n",
       "3 3.68      3.27       4.89    4.75      ⋯ 2.26      2.37      8.97    \n",
       "4 1.44      0.89       1.52    1.61      ⋯ 0.65      0.68      1.43    \n",
       "5 0.71      0.57       1.00    1.64      ⋯ 0.45      0.50      4.22    \n",
       "6 1.32      1.05       0.93    1.01      ⋯ 0.36      3.15      3.78    \n",
       "  7316-2744 7316-1116 7316-333 7316-775 7316-96 7316-1750 7316-3963\n",
       "1 11.24     7.41      29.74    3.04     5.81    2.59      1.38     \n",
       "2  0.53     0.01       0.02    0.00     0.01    0.01      0.00     \n",
       "3  4.07     8.08      29.66    2.58     7.43    3.14      2.83     \n",
       "4  1.38     2.05       9.99    1.52     2.62    1.40      0.71     \n",
       "5  0.71     0.98       7.38    0.82     1.69    1.08      0.65     \n",
       "6  0.44     1.51       2.06    0.19     0.53    1.54      5.57     "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "head(CBTTCtpm)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "CBTTCtpm <- cbind(NA, NA, CBTTCtpm)\n",
    "colnames(CBTTCtpm)[1:2] <- c(\"ensembl_id\", \"hgnc_symbol\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "CBTTCtpm$hgnc_symbol <- gsub(\".*_\", \"\", CBTTCtpm$`Var.3`)\n",
    "CBTTCtpm$ensembl_id <- gsub(\"_.*\", \"\", CBTTCtpm$`Var.3`)\n",
    "CBTTCtpm$`Var.3` <- NULL"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<style>\n",
       ".list-inline {list-style: none; margin:0; padding: 0}\n",
       ".list-inline>li {display: inline-block}\n",
       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "</style>\n",
       "<ol class=list-inline><li>58347</li><li>971</li></ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 58347\n",
       "\\item 971\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 58347\n",
       "2. 971\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 58347   971"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "dim(CBTTCtpm)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "CBTTCtpm <- CBTTCtpm[!duplicated(CBTTCtpm$hgnc_symbol),]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "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>56505</li><li>971</li></ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 56505\n",
       "\\item 971\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 56505\n",
       "2. 971\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 56505   971"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "dim(CBTTCtpm)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table class=\"dataframe\">\n",
       "<caption>A data.frame: 6 × 971</caption>\n",
       "<thead>\n",
       "\t<tr><th></th><th scope=col>ensembl_id</th><th scope=col>hgnc_symbol</th><th scope=col>7316-2599</th><th scope=col>7316-1926</th><th scope=col>7316-489</th><th scope=col>7316-16</th><th scope=col>7316-13</th><th scope=col>7316-3936</th><th scope=col>7316-3632</th><th scope=col>7316-873</th><th scope=col>⋯</th><th scope=col>7316-2589</th><th scope=col>7316-395</th><th scope=col>7316-1785</th><th scope=col>7316-2744</th><th scope=col>7316-1116</th><th scope=col>7316-333</th><th scope=col>7316-775</th><th scope=col>7316-96</th><th scope=col>7316-1750</th><th scope=col>7316-3963</th></tr>\n",
       "\t<tr><th></th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>⋯</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;dbl&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>1</th><td>ENSG00000000003.14</td><td>TSPAN6  </td><td>10.99</td><td>8.66</td><td>6.15</td><td>2.40</td><td>0.73</td><td>1.50</td><td>1.88</td><td>29.41</td><td>⋯</td><td>2.36</td><td>2.76</td><td>12.78</td><td>11.24</td><td>7.41</td><td>29.74</td><td>3.04</td><td>5.81</td><td>2.59</td><td>1.38</td></tr>\n",
       "\t<tr><th scope=row>2</th><td>ENSG00000000005.5 </td><td>TNMD    </td><td> 0.18</td><td>0.02</td><td>0.03</td><td>0.02</td><td>0.02</td><td>0.01</td><td>0.03</td><td> 0.33</td><td>⋯</td><td>0.00</td><td>0.02</td><td> 0.01</td><td> 0.53</td><td>0.01</td><td> 0.02</td><td>0.00</td><td>0.01</td><td>0.01</td><td>0.00</td></tr>\n",
       "\t<tr><th scope=row>3</th><td>ENSG00000000419.12</td><td>DPM1    </td><td> 4.95</td><td>6.15</td><td>5.09</td><td>3.35</td><td>1.09</td><td>3.68</td><td>3.27</td><td> 4.89</td><td>⋯</td><td>2.26</td><td>2.37</td><td> 8.97</td><td> 4.07</td><td>8.08</td><td>29.66</td><td>2.58</td><td>7.43</td><td>3.14</td><td>2.83</td></tr>\n",
       "\t<tr><th scope=row>4</th><td>ENSG00000000457.13</td><td>SCYL3   </td><td> 1.50</td><td>1.75</td><td>1.71</td><td>0.90</td><td>0.44</td><td>1.44</td><td>0.89</td><td> 1.52</td><td>⋯</td><td>0.65</td><td>0.68</td><td> 1.43</td><td> 1.38</td><td>2.05</td><td> 9.99</td><td>1.52</td><td>2.62</td><td>1.40</td><td>0.71</td></tr>\n",
       "\t<tr><th scope=row>5</th><td>ENSG00000000460.16</td><td>C1orf112</td><td> 1.70</td><td>1.12</td><td>2.78</td><td>0.34</td><td>0.43</td><td>0.71</td><td>0.57</td><td> 1.00</td><td>⋯</td><td>0.45</td><td>0.50</td><td> 4.22</td><td> 0.71</td><td>0.98</td><td> 7.38</td><td>0.82</td><td>1.69</td><td>1.08</td><td>0.65</td></tr>\n",
       "\t<tr><th scope=row>6</th><td>ENSG00000000938.12</td><td>FGR     </td><td> 1.27</td><td>0.90</td><td>0.18</td><td>1.12</td><td>0.36</td><td>1.32</td><td>1.05</td><td> 0.93</td><td>⋯</td><td>0.36</td><td>3.15</td><td> 3.78</td><td> 0.44</td><td>1.51</td><td> 2.06</td><td>0.19</td><td>0.53</td><td>1.54</td><td>5.57</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.frame: 6 × 971\n",
       "\\begin{tabular}{r|lllllllllllllllllllll}\n",
       "  & ensembl\\_id & hgnc\\_symbol & 7316-2599 & 7316-1926 & 7316-489 & 7316-16 & 7316-13 & 7316-3936 & 7316-3632 & 7316-873 & ⋯ & 7316-2589 & 7316-395 & 7316-1785 & 7316-2744 & 7316-1116 & 7316-333 & 7316-775 & 7316-96 & 7316-1750 & 7316-3963\\\\\n",
       "  & <chr> & <chr> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & ⋯ & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl>\\\\\n",
       "\\hline\n",
       "\t1 & ENSG00000000003.14 & TSPAN6   & 10.99 & 8.66 & 6.15 & 2.40 & 0.73 & 1.50 & 1.88 & 29.41 & ⋯ & 2.36 & 2.76 & 12.78 & 11.24 & 7.41 & 29.74 & 3.04 & 5.81 & 2.59 & 1.38\\\\\n",
       "\t2 & ENSG00000000005.5  & TNMD     &  0.18 & 0.02 & 0.03 & 0.02 & 0.02 & 0.01 & 0.03 &  0.33 & ⋯ & 0.00 & 0.02 &  0.01 &  0.53 & 0.01 &  0.02 & 0.00 & 0.01 & 0.01 & 0.00\\\\\n",
       "\t3 & ENSG00000000419.12 & DPM1     &  4.95 & 6.15 & 5.09 & 3.35 & 1.09 & 3.68 & 3.27 &  4.89 & ⋯ & 2.26 & 2.37 &  8.97 &  4.07 & 8.08 & 29.66 & 2.58 & 7.43 & 3.14 & 2.83\\\\\n",
       "\t4 & ENSG00000000457.13 & SCYL3    &  1.50 & 1.75 & 1.71 & 0.90 & 0.44 & 1.44 & 0.89 &  1.52 & ⋯ & 0.65 & 0.68 &  1.43 &  1.38 & 2.05 &  9.99 & 1.52 & 2.62 & 1.40 & 0.71\\\\\n",
       "\t5 & ENSG00000000460.16 & C1orf112 &  1.70 & 1.12 & 2.78 & 0.34 & 0.43 & 0.71 & 0.57 &  1.00 & ⋯ & 0.45 & 0.50 &  4.22 &  0.71 & 0.98 &  7.38 & 0.82 & 1.69 & 1.08 & 0.65\\\\\n",
       "\t6 & ENSG00000000938.12 & FGR      &  1.27 & 0.90 & 0.18 & 1.12 & 0.36 & 1.32 & 1.05 &  0.93 & ⋯ & 0.36 & 3.15 &  3.78 &  0.44 & 1.51 &  2.06 & 0.19 & 0.53 & 1.54 & 5.57\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.frame: 6 × 971\n",
       "\n",
       "| <!--/--> | ensembl_id &lt;chr&gt; | hgnc_symbol &lt;chr&gt; | 7316-2599 &lt;dbl&gt; | 7316-1926 &lt;dbl&gt; | 7316-489 &lt;dbl&gt; | 7316-16 &lt;dbl&gt; | 7316-13 &lt;dbl&gt; | 7316-3936 &lt;dbl&gt; | 7316-3632 &lt;dbl&gt; | 7316-873 &lt;dbl&gt; | ⋯ ⋯ | 7316-2589 &lt;dbl&gt; | 7316-395 &lt;dbl&gt; | 7316-1785 &lt;dbl&gt; | 7316-2744 &lt;dbl&gt; | 7316-1116 &lt;dbl&gt; | 7316-333 &lt;dbl&gt; | 7316-775 &lt;dbl&gt; | 7316-96 &lt;dbl&gt; | 7316-1750 &lt;dbl&gt; | 7316-3963 &lt;dbl&gt; |\n",
       "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
       "| 1 | ENSG00000000003.14 | TSPAN6   | 10.99 | 8.66 | 6.15 | 2.40 | 0.73 | 1.50 | 1.88 | 29.41 | ⋯ | 2.36 | 2.76 | 12.78 | 11.24 | 7.41 | 29.74 | 3.04 | 5.81 | 2.59 | 1.38 |\n",
       "| 2 | ENSG00000000005.5  | TNMD     |  0.18 | 0.02 | 0.03 | 0.02 | 0.02 | 0.01 | 0.03 |  0.33 | ⋯ | 0.00 | 0.02 |  0.01 |  0.53 | 0.01 |  0.02 | 0.00 | 0.01 | 0.01 | 0.00 |\n",
       "| 3 | ENSG00000000419.12 | DPM1     |  4.95 | 6.15 | 5.09 | 3.35 | 1.09 | 3.68 | 3.27 |  4.89 | ⋯ | 2.26 | 2.37 |  8.97 |  4.07 | 8.08 | 29.66 | 2.58 | 7.43 | 3.14 | 2.83 |\n",
       "| 4 | ENSG00000000457.13 | SCYL3    |  1.50 | 1.75 | 1.71 | 0.90 | 0.44 | 1.44 | 0.89 |  1.52 | ⋯ | 0.65 | 0.68 |  1.43 |  1.38 | 2.05 |  9.99 | 1.52 | 2.62 | 1.40 | 0.71 |\n",
       "| 5 | ENSG00000000460.16 | C1orf112 |  1.70 | 1.12 | 2.78 | 0.34 | 0.43 | 0.71 | 0.57 |  1.00 | ⋯ | 0.45 | 0.50 |  4.22 |  0.71 | 0.98 |  7.38 | 0.82 | 1.69 | 1.08 | 0.65 |\n",
       "| 6 | ENSG00000000938.12 | FGR      |  1.27 | 0.90 | 0.18 | 1.12 | 0.36 | 1.32 | 1.05 |  0.93 | ⋯ | 0.36 | 3.15 |  3.78 |  0.44 | 1.51 |  2.06 | 0.19 | 0.53 | 1.54 | 5.57 |\n",
       "\n"
      ],
      "text/plain": [
       "  ensembl_id         hgnc_symbol 7316-2599 7316-1926 7316-489 7316-16 7316-13\n",
       "1 ENSG00000000003.14 TSPAN6      10.99     8.66      6.15     2.40    0.73   \n",
       "2 ENSG00000000005.5  TNMD         0.18     0.02      0.03     0.02    0.02   \n",
       "3 ENSG00000000419.12 DPM1         4.95     6.15      5.09     3.35    1.09   \n",
       "4 ENSG00000000457.13 SCYL3        1.50     1.75      1.71     0.90    0.44   \n",
       "5 ENSG00000000460.16 C1orf112     1.70     1.12      2.78     0.34    0.43   \n",
       "6 ENSG00000000938.12 FGR          1.27     0.90      0.18     1.12    0.36   \n",
       "  7316-3936 7316-3632 7316-873 ⋯ 7316-2589 7316-395 7316-1785 7316-2744\n",
       "1 1.50      1.88      29.41    ⋯ 2.36      2.76     12.78     11.24    \n",
       "2 0.01      0.03       0.33    ⋯ 0.00      0.02      0.01      0.53    \n",
       "3 3.68      3.27       4.89    ⋯ 2.26      2.37      8.97      4.07    \n",
       "4 1.44      0.89       1.52    ⋯ 0.65      0.68      1.43      1.38    \n",
       "5 0.71      0.57       1.00    ⋯ 0.45      0.50      4.22      0.71    \n",
       "6 1.32      1.05       0.93    ⋯ 0.36      3.15      3.78      0.44    \n",
       "  7316-1116 7316-333 7316-775 7316-96 7316-1750 7316-3963\n",
       "1 7.41      29.74    3.04     5.81    2.59      1.38     \n",
       "2 0.01       0.02    0.00     0.01    0.01      0.00     \n",
       "3 8.08      29.66    2.58     7.43    3.14      2.83     \n",
       "4 2.05       9.99    1.52     2.62    1.40      0.71     \n",
       "5 0.98       7.38    0.82     1.69    1.08      0.65     \n",
       "6 1.51       2.06    0.19     0.53    1.54      5.57     "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "head(CBTTCtpm)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
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   ],
   "source": [
    "CBTTCtpm[ CBTTCtpm$hgnc_symbol == \"DAZ1\", \"7316-905\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "write.table(CBTTCtpm,\n",
    "            file = paste0(datapath, \"exp_mat/CBTTC_tpm_matrix_dedup.txt\"),\n",
    "                sep = \"\\t\", quote = F, row.names = F)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "write.table(CBTTCtpm[,colnames(CBTTCtpm) !=\"ensembl_id\"],\n",
    "            file = paste0(datapath, \"exp_mat/CBTTC_tpm_matrix_dedup_hgnc.txt\"),\n",
    "                sep = \"\\t\", quote = F, row.names = F)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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