{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# File I/O"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Registered S3 methods overwritten by 'ggplot2':\n",
      "  method         from \n",
      "  [.quosures     rlang\n",
      "  c.quosures     rlang\n",
      "  print.quosures rlang\n",
      "── \u001b[1mAttaching packages\u001b[22m ─────────────────────────────────────── tidyverse 1.2.1 ──\n",
      "\u001b[32m✔\u001b[39m \u001b[34mggplot2\u001b[39m 3.1.1     \u001b[32m✔\u001b[39m \u001b[34mpurrr  \u001b[39m 0.3.2\n",
      "\u001b[32m✔\u001b[39m \u001b[34mtibble \u001b[39m 2.1.2     \u001b[32m✔\u001b[39m \u001b[34mdplyr  \u001b[39m 0.8.1\n",
      "\u001b[32m✔\u001b[39m \u001b[34mtidyr  \u001b[39m 0.8.3     \u001b[32m✔\u001b[39m \u001b[34mstringr\u001b[39m 1.4.0\n",
      "\u001b[32m✔\u001b[39m \u001b[34mreadr  \u001b[39m 1.3.1     \u001b[32m✔\u001b[39m \u001b[34mforcats\u001b[39m 0.4.0\n",
      "── \u001b[1mConflicts\u001b[22m ────────────────────────────────────────── tidyverse_conflicts() ──\n",
      "\u001b[31m✖\u001b[39m \u001b[34mdplyr\u001b[39m::\u001b[32mfilter()\u001b[39m masks \u001b[34mstats\u001b[39m::filter()\n",
      "\u001b[31m✖\u001b[39m \u001b[34mdplyr\u001b[39m::\u001b[32mlag()\u001b[39m    masks \u001b[34mstats\u001b[39m::lag()\n"
     ]
    }
   ],
   "source": [
    "library(tidyverse)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Strucrure of count data from STAR"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "- column 1: gene ID\n",
    "- column 2: counts for unstranded RNA-seq\n",
    "- column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes)\n",
    "- column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Get list of files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "count_dir <- \"/data/hts_2019_data/hts2019_pilot_counts\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "files <- list.files(path=count_dir, pattern=\"*.tab\", full.names = TRUE)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "'/data/hts_2019_data/hts2019_pilot_counts/1_2019_P_M1_S1_L001_ReadsPerGene.out.tab'"
      ],
      "text/latex": [
       "'/data/hts\\_2019\\_data/hts2019\\_pilot\\_counts/1\\_2019\\_P\\_M1\\_S1\\_L001\\_ReadsPerGene.out.tab'"
      ],
      "text/markdown": [
       "'/data/hts_2019_data/hts2019_pilot_counts/1_2019_P_M1_S1_L001_ReadsPerGene.out.tab'"
      ],
      "text/plain": [
       "[1] \"/data/hts_2019_data/hts2019_pilot_counts/1_2019_P_M1_S1_L001_ReadsPerGene.out.tab\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "files[1]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Read in first 2 files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "d1 <- read_tsv(files[1], col_names=FALSE, col_type=cols())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "d2 <- read_tsv(files[2], col_names=FALSE, col_type=cols())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A tibble: 5 × 4</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>X1</th><th scope=col>X2</th><th scope=col>X3</th><th scope=col>X4</th></tr>\n",
       "\t<tr><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></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>N_unmapped    </td><td> 21162</td><td>  21162</td><td>21162</td></tr>\n",
       "\t<tr><td>N_multimapping</td><td> 95540</td><td>  95540</td><td>95540</td></tr>\n",
       "\t<tr><td>N_noFeature   </td><td> 17075</td><td>4260222</td><td>26923</td></tr>\n",
       "\t<tr><td>N_ambiguous   </td><td>418493</td><td>   1416</td><td>  606</td></tr>\n",
       "\t<tr><td>CNAG_04548    </td><td>     0</td><td>      0</td><td>    0</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A tibble: 5 × 4\n",
       "\\begin{tabular}{r|llll}\n",
       " X1 & X2 & X3 & X4\\\\\n",
       " <chr> & <dbl> & <dbl> & <dbl>\\\\\n",
       "\\hline\n",
       "\t N\\_unmapped     &  21162 &   21162 & 21162\\\\\n",
       "\t N\\_multimapping &  95540 &   95540 & 95540\\\\\n",
       "\t N\\_noFeature    &  17075 & 4260222 & 26923\\\\\n",
       "\t N\\_ambiguous    & 418493 &    1416 &   606\\\\\n",
       "\t CNAG\\_04548     &      0 &       0 &     0\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A tibble: 5 × 4\n",
       "\n",
       "| X1 &lt;chr&gt; | X2 &lt;dbl&gt; | X3 &lt;dbl&gt; | X4 &lt;dbl&gt; |\n",
       "|---|---|---|---|\n",
       "| N_unmapped     |  21162 |   21162 | 21162 |\n",
       "| N_multimapping |  95540 |   95540 | 95540 |\n",
       "| N_noFeature    |  17075 | 4260222 | 26923 |\n",
       "| N_ambiguous    | 418493 |    1416 |   606 |\n",
       "| CNAG_04548     |      0 |       0 |     0 |\n",
       "\n"
      ],
      "text/plain": [
       "  X1             X2     X3      X4   \n",
       "1 N_unmapped      21162   21162 21162\n",
       "2 N_multimapping  95540   95540 95540\n",
       "3 N_noFeature     17075 4260222 26923\n",
       "4 N_ambiguous    418493    1416   606\n",
       "5 CNAG_04548          0       0     0"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "d1 %>% head(5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A tibble: 5 × 4</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>X1</th><th scope=col>X2</th><th scope=col>X3</th><th scope=col>X4</th></tr>\n",
       "\t<tr><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></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>N_unmapped    </td><td> 19644</td><td>  19644</td><td>19644</td></tr>\n",
       "\t<tr><td>N_multimapping</td><td> 94070</td><td>  94070</td><td>94070</td></tr>\n",
       "\t<tr><td>N_noFeature   </td><td> 16407</td><td>4195892</td><td>26053</td></tr>\n",
       "\t<tr><td>N_ambiguous   </td><td>412656</td><td>   1410</td><td>  638</td></tr>\n",
       "\t<tr><td>CNAG_04548    </td><td>     0</td><td>      0</td><td>    0</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A tibble: 5 × 4\n",
       "\\begin{tabular}{r|llll}\n",
       " X1 & X2 & X3 & X4\\\\\n",
       " <chr> & <dbl> & <dbl> & <dbl>\\\\\n",
       "\\hline\n",
       "\t N\\_unmapped     &  19644 &   19644 & 19644\\\\\n",
       "\t N\\_multimapping &  94070 &   94070 & 94070\\\\\n",
       "\t N\\_noFeature    &  16407 & 4195892 & 26053\\\\\n",
       "\t N\\_ambiguous    & 412656 &    1410 &   638\\\\\n",
       "\t CNAG\\_04548     &      0 &       0 &     0\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A tibble: 5 × 4\n",
       "\n",
       "| X1 &lt;chr&gt; | X2 &lt;dbl&gt; | X3 &lt;dbl&gt; | X4 &lt;dbl&gt; |\n",
       "|---|---|---|---|\n",
       "| N_unmapped     |  19644 |   19644 | 19644 |\n",
       "| N_multimapping |  94070 |   94070 | 94070 |\n",
       "| N_noFeature    |  16407 | 4195892 | 26053 |\n",
       "| N_ambiguous    | 412656 |    1410 |   638 |\n",
       "| CNAG_04548     |      0 |       0 |     0 |\n",
       "\n"
      ],
      "text/plain": [
       "  X1             X2     X3      X4   \n",
       "1 N_unmapped      19644   19644 19644\n",
       "2 N_multimapping  94070   94070 94070\n",
       "3 N_noFeature     16407 4195892 26053\n",
       "4 N_ambiguous    412656    1410   638\n",
       "5 CNAG_04548          0       0     0"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "d2 %>% head(5)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Combining files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A tibble: 5 × 8</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>X1</th><th scope=col>X2</th><th scope=col>X3</th><th scope=col>X4</th><th scope=col>X11</th><th scope=col>X21</th><th scope=col>X31</th><th scope=col>X41</th></tr>\n",
       "\t<tr><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;chr&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><td>N_unmapped    </td><td> 21162</td><td>  21162</td><td>21162</td><td>N_unmapped    </td><td> 19644</td><td>  19644</td><td>19644</td></tr>\n",
       "\t<tr><td>N_multimapping</td><td> 95540</td><td>  95540</td><td>95540</td><td>N_multimapping</td><td> 94070</td><td>  94070</td><td>94070</td></tr>\n",
       "\t<tr><td>N_noFeature   </td><td> 17075</td><td>4260222</td><td>26923</td><td>N_noFeature   </td><td> 16407</td><td>4195892</td><td>26053</td></tr>\n",
       "\t<tr><td>N_ambiguous   </td><td>418493</td><td>   1416</td><td>  606</td><td>N_ambiguous   </td><td>412656</td><td>   1410</td><td>  638</td></tr>\n",
       "\t<tr><td>CNAG_04548    </td><td>     0</td><td>      0</td><td>    0</td><td>CNAG_04548    </td><td>     0</td><td>      0</td><td>    0</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A tibble: 5 × 8\n",
       "\\begin{tabular}{r|llllllll}\n",
       " X1 & X2 & X3 & X4 & X11 & X21 & X31 & X41\\\\\n",
       " <chr> & <dbl> & <dbl> & <dbl> & <chr> & <dbl> & <dbl> & <dbl>\\\\\n",
       "\\hline\n",
       "\t N\\_unmapped     &  21162 &   21162 & 21162 & N\\_unmapped     &  19644 &   19644 & 19644\\\\\n",
       "\t N\\_multimapping &  95540 &   95540 & 95540 & N\\_multimapping &  94070 &   94070 & 94070\\\\\n",
       "\t N\\_noFeature    &  17075 & 4260222 & 26923 & N\\_noFeature    &  16407 & 4195892 & 26053\\\\\n",
       "\t N\\_ambiguous    & 418493 &    1416 &   606 & N\\_ambiguous    & 412656 &    1410 &   638\\\\\n",
       "\t CNAG\\_04548     &      0 &       0 &     0 & CNAG\\_04548     &      0 &       0 &     0\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A tibble: 5 × 8\n",
       "\n",
       "| X1 &lt;chr&gt; | X2 &lt;dbl&gt; | X3 &lt;dbl&gt; | X4 &lt;dbl&gt; | X11 &lt;chr&gt; | X21 &lt;dbl&gt; | X31 &lt;dbl&gt; | X41 &lt;dbl&gt; |\n",
       "|---|---|---|---|---|---|---|---|\n",
       "| N_unmapped     |  21162 |   21162 | 21162 | N_unmapped     |  19644 |   19644 | 19644 |\n",
       "| N_multimapping |  95540 |   95540 | 95540 | N_multimapping |  94070 |   94070 | 94070 |\n",
       "| N_noFeature    |  17075 | 4260222 | 26923 | N_noFeature    |  16407 | 4195892 | 26053 |\n",
       "| N_ambiguous    | 418493 |    1416 |   606 | N_ambiguous    | 412656 |    1410 |   638 |\n",
       "| CNAG_04548     |      0 |       0 |     0 | CNAG_04548     |      0 |       0 |     0 |\n",
       "\n"
      ],
      "text/plain": [
       "  X1             X2     X3      X4    X11            X21    X31     X41  \n",
       "1 N_unmapped      21162   21162 21162 N_unmapped      19644   19644 19644\n",
       "2 N_multimapping  95540   95540 95540 N_multimapping  94070   94070 94070\n",
       "3 N_noFeature     17075 4260222 26923 N_noFeature     16407 4195892 26053\n",
       "4 N_ambiguous    418493    1416   606 N_ambiguous    412656    1410   638\n",
       "5 CNAG_04548          0       0     0 CNAG_04548          0       0     0"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "bind_cols(d1, d2) %>% head(5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A tibble: 5 × 4</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>X1</th><th scope=col>X2</th><th scope=col>X3</th><th scope=col>X4</th></tr>\n",
       "\t<tr><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></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>N_unmapped    </td><td> 21162</td><td>  21162</td><td>21162</td></tr>\n",
       "\t<tr><td>N_multimapping</td><td> 95540</td><td>  95540</td><td>95540</td></tr>\n",
       "\t<tr><td>N_noFeature   </td><td> 17075</td><td>4260222</td><td>26923</td></tr>\n",
       "\t<tr><td>N_ambiguous   </td><td>418493</td><td>   1416</td><td>  606</td></tr>\n",
       "\t<tr><td>CNAG_04548    </td><td>     0</td><td>      0</td><td>    0</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A tibble: 5 × 4\n",
       "\\begin{tabular}{r|llll}\n",
       " X1 & X2 & X3 & X4\\\\\n",
       " <chr> & <dbl> & <dbl> & <dbl>\\\\\n",
       "\\hline\n",
       "\t N\\_unmapped     &  21162 &   21162 & 21162\\\\\n",
       "\t N\\_multimapping &  95540 &   95540 & 95540\\\\\n",
       "\t N\\_noFeature    &  17075 & 4260222 & 26923\\\\\n",
       "\t N\\_ambiguous    & 418493 &    1416 &   606\\\\\n",
       "\t CNAG\\_04548     &      0 &       0 &     0\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A tibble: 5 × 4\n",
       "\n",
       "| X1 &lt;chr&gt; | X2 &lt;dbl&gt; | X3 &lt;dbl&gt; | X4 &lt;dbl&gt; |\n",
       "|---|---|---|---|\n",
       "| N_unmapped     |  21162 |   21162 | 21162 |\n",
       "| N_multimapping |  95540 |   95540 | 95540 |\n",
       "| N_noFeature    |  17075 | 4260222 | 26923 |\n",
       "| N_ambiguous    | 418493 |    1416 |   606 |\n",
       "| CNAG_04548     |      0 |       0 |     0 |\n",
       "\n"
      ],
      "text/plain": [
       "  X1             X2     X3      X4   \n",
       "1 N_unmapped      21162   21162 21162\n",
       "2 N_multimapping  95540   95540 95540\n",
       "3 N_noFeature     17075 4260222 26923\n",
       "4 N_ambiguous    418493    1416   606\n",
       "5 CNAG_04548          0       0     0"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "bind_rows(d1, d2) %>% head(5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A tibble: 5 × 7</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>X1</th><th scope=col>X2.x</th><th scope=col>X3.x</th><th scope=col>X4.x</th><th scope=col>X2.y</th><th scope=col>X3.y</th><th scope=col>X4.y</th></tr>\n",
       "\t<tr><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></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>N_unmapped    </td><td> 21162</td><td>  21162</td><td>21162</td><td> 19644</td><td>  19644</td><td>19644</td></tr>\n",
       "\t<tr><td>N_multimapping</td><td> 95540</td><td>  95540</td><td>95540</td><td> 94070</td><td>  94070</td><td>94070</td></tr>\n",
       "\t<tr><td>N_noFeature   </td><td> 17075</td><td>4260222</td><td>26923</td><td> 16407</td><td>4195892</td><td>26053</td></tr>\n",
       "\t<tr><td>N_ambiguous   </td><td>418493</td><td>   1416</td><td>  606</td><td>412656</td><td>   1410</td><td>  638</td></tr>\n",
       "\t<tr><td>CNAG_04548    </td><td>     0</td><td>      0</td><td>    0</td><td>     0</td><td>      0</td><td>    0</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A tibble: 5 × 7\n",
       "\\begin{tabular}{r|lllllll}\n",
       " X1 & X2.x & X3.x & X4.x & X2.y & X3.y & X4.y\\\\\n",
       " <chr> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl>\\\\\n",
       "\\hline\n",
       "\t N\\_unmapped     &  21162 &   21162 & 21162 &  19644 &   19644 & 19644\\\\\n",
       "\t N\\_multimapping &  95540 &   95540 & 95540 &  94070 &   94070 & 94070\\\\\n",
       "\t N\\_noFeature    &  17075 & 4260222 & 26923 &  16407 & 4195892 & 26053\\\\\n",
       "\t N\\_ambiguous    & 418493 &    1416 &   606 & 412656 &    1410 &   638\\\\\n",
       "\t CNAG\\_04548     &      0 &       0 &     0 &      0 &       0 &     0\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A tibble: 5 × 7\n",
       "\n",
       "| X1 &lt;chr&gt; | X2.x &lt;dbl&gt; | X3.x &lt;dbl&gt; | X4.x &lt;dbl&gt; | X2.y &lt;dbl&gt; | X3.y &lt;dbl&gt; | X4.y &lt;dbl&gt; |\n",
       "|---|---|---|---|---|---|---|\n",
       "| N_unmapped     |  21162 |   21162 | 21162 |  19644 |   19644 | 19644 |\n",
       "| N_multimapping |  95540 |   95540 | 95540 |  94070 |   94070 | 94070 |\n",
       "| N_noFeature    |  17075 | 4260222 | 26923 |  16407 | 4195892 | 26053 |\n",
       "| N_ambiguous    | 418493 |    1416 |   606 | 412656 |    1410 |   638 |\n",
       "| CNAG_04548     |      0 |       0 |     0 |      0 |       0 |     0 |\n",
       "\n"
      ],
      "text/plain": [
       "  X1             X2.x   X3.x    X4.x  X2.y   X3.y    X4.y \n",
       "1 N_unmapped      21162   21162 21162  19644   19644 19644\n",
       "2 N_multimapping  95540   95540 95540  94070   94070 94070\n",
       "3 N_noFeature     17075 4260222 26923  16407 4195892 26053\n",
       "4 N_ambiguous    418493    1416   606 412656    1410   638\n",
       "5 CNAG_04548          0       0     0      0       0     0"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "inner_join(x=d1, y=d2, by='X1') %>% head(5)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Custom function to read files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "read_file <- function(file) {\n",
    "    read_tsv(file, col_names = FALSE, skip=4, col_types = cols()) %>%\n",
    "    mutate(source=basename(file)) %>%\n",
    "    select(source=source, gene=X1, count=X4) %>%\n",
    "    separate(source, sep='_', into=c(\"sample\", \"year\", \"p\", \"method\", \"s\", \"lane\", \"junk\")) %>%\n",
    "    select(sample, year, p, method, s, lane, gene, count)\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A tibble: 5 × 8</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>sample</th><th scope=col>year</th><th scope=col>p</th><th scope=col>method</th><th scope=col>s</th><th scope=col>lane</th><th scope=col>gene</th><th scope=col>count</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;dbl&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>1</td><td>2019</td><td>P</td><td>M1</td><td>S1</td><td>L001</td><td>CNAG_04548</td><td> 0</td></tr>\n",
       "\t<tr><td>1</td><td>2019</td><td>P</td><td>M1</td><td>S1</td><td>L001</td><td>CNAG_07303</td><td> 0</td></tr>\n",
       "\t<tr><td>1</td><td>2019</td><td>P</td><td>M1</td><td>S1</td><td>L001</td><td>CNAG_07304</td><td>14</td></tr>\n",
       "\t<tr><td>1</td><td>2019</td><td>P</td><td>M1</td><td>S1</td><td>L001</td><td>CNAG_00001</td><td> 0</td></tr>\n",
       "\t<tr><td>1</td><td>2019</td><td>P</td><td>M1</td><td>S1</td><td>L001</td><td>CNAG_07305</td><td> 1</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A tibble: 5 × 8\n",
       "\\begin{tabular}{r|llllllll}\n",
       " sample & year & p & method & s & lane & gene & count\\\\\n",
       " <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <dbl>\\\\\n",
       "\\hline\n",
       "\t 1 & 2019 & P & M1 & S1 & L001 & CNAG\\_04548 &  0\\\\\n",
       "\t 1 & 2019 & P & M1 & S1 & L001 & CNAG\\_07303 &  0\\\\\n",
       "\t 1 & 2019 & P & M1 & S1 & L001 & CNAG\\_07304 & 14\\\\\n",
       "\t 1 & 2019 & P & M1 & S1 & L001 & CNAG\\_00001 &  0\\\\\n",
       "\t 1 & 2019 & P & M1 & S1 & L001 & CNAG\\_07305 &  1\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A tibble: 5 × 8\n",
       "\n",
       "| sample &lt;chr&gt; | year &lt;chr&gt; | p &lt;chr&gt; | method &lt;chr&gt; | s &lt;chr&gt; | lane &lt;chr&gt; | gene &lt;chr&gt; | count &lt;dbl&gt; |\n",
       "|---|---|---|---|---|---|---|---|\n",
       "| 1 | 2019 | P | M1 | S1 | L001 | CNAG_04548 |  0 |\n",
       "| 1 | 2019 | P | M1 | S1 | L001 | CNAG_07303 |  0 |\n",
       "| 1 | 2019 | P | M1 | S1 | L001 | CNAG_07304 | 14 |\n",
       "| 1 | 2019 | P | M1 | S1 | L001 | CNAG_00001 |  0 |\n",
       "| 1 | 2019 | P | M1 | S1 | L001 | CNAG_07305 |  1 |\n",
       "\n"
      ],
      "text/plain": [
       "  sample year p method s  lane gene       count\n",
       "1 1      2019 P M1     S1 L001 CNAG_04548  0   \n",
       "2 1      2019 P M1     S1 L001 CNAG_07303  0   \n",
       "3 1      2019 P M1     S1 L001 CNAG_07304 14   \n",
       "4 1      2019 P M1     S1 L001 CNAG_00001  0   \n",
       "5 1      2019 P M1     S1 L001 CNAG_07305  1   "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "read_file(files[1]) %>% head(5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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