5_Chi_Squared_feature_selection_methylation450K.ipynb

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      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
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      "source": [
        "<a href=\"https://colab.research.google.com/github/nadunchanna98/MultiOmics-CervicalCancer-MachineLearning-DataProcessing/blob/main/Chi_Squared_feature_selection_methylation450K.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "46131d15",
      "metadata": {
        "id": "46131d15",
        "outputId": "dc6c1c24-b08e-4d77-d758-4e5ddfb35d07"
      },
      "outputs": [
        {
          "name": "stderr",
          "output_type": "stream",
          "text": [
            "C:\\Users\\PC\\AppData\\Local\\Temp\\ipykernel_4536\\1675183931.py:4: DtypeWarning: Columns (1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312) have mixed types. Specify dtype option on import or set low_memory=False.\n",
            "  df = pd.read_csv('Downloads/merged_data2_methilation450K.csv')\n"
          ]
        }
      ],
      "source": [
        "import pandas as pd\n",
        "\n",
        "# Read the CSV file into a DataFrame\n",
        "df = pd.read_csv('Downloads/merged_data2_methilation450K.csv')"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "8424f7a9",
      "metadata": {
        "id": "8424f7a9",
        "outputId": "78b0b702-e1e5-484f-dc94-1ec24d2fb03d"
      },
      "outputs": [
        {
          "data": {
            "text/plain": [
              "(372139, 313)"
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          },
          "execution_count": 7,
          "metadata": {},
          "output_type": "execute_result"
        }
      ],
      "source": [
        "df.shape"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "e28caeb1",
      "metadata": {
        "id": "e28caeb1"
      },
      "outputs": [],
      "source": [
        "import numpy as np\n",
        "import pandas as pd\n",
        "import seaborn as sns\n",
        "import matplotlib.pyplot as plt"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "0ce8640f",
      "metadata": {
        "id": "0ce8640f",
        "outputId": "3c70bcdf-b293-4ca9-c65c-9bb0c1bdc5dc"
      },
      "outputs": [
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              "      <th></th>\n",
              "      <th>SampleID</th>\n",
              "      <th>TCGA-EK-A3GK-01</th>\n",
              "      <th>TCGA-GH-A9DA-01</th>\n",
              "      <th>TCGA-VS-A94Y-01</th>\n",
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              "      <td>histological_type</td>\n",
              "      <td>Endocervical Type of Adenocarcinoma</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>Endocervical Type of Adenocarcinoma</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>Endocervical Type of Adenocarcinoma</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>...</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>Endocervical Type of Adenocarcinoma</td>\n",
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              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>cg13332474</td>\n",
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              "      <td>0.0298</td>\n",
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              "      <td>0.0492</td>\n",
              "      <td>0.0274</td>\n",
              "      <td>0.3471</td>\n",
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              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>cg00651829</td>\n",
              "      <td>0.1921</td>\n",
              "      <td>0.6911</td>\n",
              "      <td>0.0189</td>\n",
              "      <td>0.0202</td>\n",
              "      <td>0.0164</td>\n",
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              "      <td>0.0223</td>\n",
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              "      <td>0.5036</td>\n",
              "      <td>0.0249</td>\n",
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              "      <td>cg11692435</td>\n",
              "      <td>0.9878</td>\n",
              "      <td>0.9861</td>\n",
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              "    <tr>\n",
              "      <th>372137</th>\n",
              "      <td>cg18138552</td>\n",
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              "    <tr>\n",
              "      <th>372138</th>\n",
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              "  </tbody>\n",
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              "<p>372138 rows × 313 columns</p>\n",
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              "0                SampleID                      TCGA-EK-A3GK-01  \\\n",
              "1       histological_type  Endocervical Type of Adenocarcinoma   \n",
              "2              cg13332474                               0.0345   \n",
              "3              cg00651829                               0.1921   \n",
              "4              cg17027195                               0.0428   \n",
              "5              cg03050183                               0.0753   \n",
              "...                   ...                                  ...   \n",
              "372134         cg11692435                               0.9878   \n",
              "372135         cg10230711                               0.0674   \n",
              "372136         cg16651827                               0.5374   \n",
              "372137         cg18138552                               0.0388   \n",
              "372138         cg07883722                               0.9557   \n",
              "\n",
              "0                        TCGA-GH-A9DA-01                   TCGA-VS-A94Y-01  \\\n",
              "1       Cervical Squamous Cell Carcinoma  Cervical Squamous Cell Carcinoma   \n",
              "2                                 0.5353                            0.0287   \n",
              "3                                 0.6911                            0.0189   \n",
              "4                                 0.0741                            0.0403   \n",
              "5                                  0.065                            0.0481   \n",
              "...                                  ...                               ...   \n",
              "372134                            0.9861                            0.9826   \n",
              "372135                             0.061                            0.0554   \n",
              "372136                             0.784                            0.7569   \n",
              "372137                            0.0312                            0.0229   \n",
              "372138                            0.9336                            0.9479   \n",
              "\n",
              "0                        TCGA-MY-A5BF-11                   TCGA-VS-A94Z-01  \\\n",
              "1       Cervical Squamous Cell Carcinoma  Cervical Squamous Cell Carcinoma   \n",
              "2                                 0.0443                            0.0296   \n",
              "3                                 0.0202                            0.0164   \n",
              "4                                 0.0403                            0.0408   \n",
              "5                                 0.2139                            0.1028   \n",
              "...                                  ...                               ...   \n",
              "372134                            0.9888                            0.9841   \n",
              "372135                            0.0482                            0.0459   \n",
              "372136                            0.7441                            0.5798   \n",
              "372137                             0.027                            0.0227   \n",
              "372138                            0.9459                            0.9462   \n",
              "\n",
              "0                           TCGA-EA-A4BA-01                   TCGA-ZJ-A8QQ-01  \\\n",
              "1       Endocervical Type of Adenocarcinoma  Cervical Squamous Cell Carcinoma   \n",
              "2                                    0.0268                            0.7356   \n",
              "3                                    0.0205                            0.5995   \n",
              "4                                     0.047                            0.8611   \n",
              "5                                    0.1044                            0.0578   \n",
              "...                                     ...                               ...   \n",
              "372134                               0.9859                            0.9821   \n",
              "372135                               0.0505                             0.042   \n",
              "372136                               0.7151                            0.8134   \n",
              "372137                                0.034                            0.0281   \n",
              "372138                               0.9517                            0.9556   \n",
              "\n",
              "0                           TCGA-FU-A3EO-11                   TCGA-DG-A2KJ-01  \\\n",
              "1       Endocervical Type of Adenocarcinoma  Cervical Squamous Cell Carcinoma   \n",
              "2                                    0.0325                             0.581   \n",
              "3                                    0.0165                            0.0223   \n",
              "4                                    0.0472                            0.0358   \n",
              "5                                      0.17                            0.1165   \n",
              "...                                     ...                               ...   \n",
              "372134                               0.9864                            0.9805   \n",
              "372135                               0.0767                            0.0884   \n",
              "372136                               0.7859                            0.8347   \n",
              "372137                               0.0251                            0.0322   \n",
              "372138                               0.9085                            0.9567   \n",
              "\n",
              "0       ...                   TCGA-C5-A1BE-01  \\\n",
              "1       ...  Cervical Squamous Cell Carcinoma   \n",
              "2       ...                            0.0275   \n",
              "3       ...                            0.0251   \n",
              "4       ...                            0.0498   \n",
              "5       ...                            0.0698   \n",
              "...     ...                               ...   \n",
              "372134  ...                            0.9796   \n",
              "372135  ...                             0.057   \n",
              "372136  ...                            0.7696   \n",
              "372137  ...                            0.0381   \n",
              "372138  ...                            0.9467   \n",
              "\n",
              "0                        TCGA-FU-A23K-01                   TCGA-C5-A1BJ-01  \\\n",
              "1       Cervical Squamous Cell Carcinoma  Cervical Squamous Cell Carcinoma   \n",
              "2                                 0.0687                            0.0303   \n",
              "3                                 0.5036                            0.0249   \n",
              "4                                 0.0495                             0.042   \n",
              "5                                 0.1205                            0.0838   \n",
              "...                                  ...                               ...   \n",
              "372134                             0.985                            0.9848   \n",
              "372135                            0.0561                            0.0664   \n",
              "372136                            0.7427                            0.7919   \n",
              "372137                            0.0299                            0.0465   \n",
              "372138                            0.9464                             0.932   \n",
              "\n",
              "0                        TCGA-FU-A23L-01                   TCGA-C5-A1M5-01  \\\n",
              "1       Cervical Squamous Cell Carcinoma  Cervical Squamous Cell Carcinoma   \n",
              "2                                 0.0298                            0.1956   \n",
              "3                                 0.0227                            0.0248   \n",
              "4                                 0.0517                            0.0597   \n",
              "5                                 0.0967                             0.069   \n",
              "...                                  ...                               ...   \n",
              "372134                            0.9845                            0.9735   \n",
              "372135                            0.0669                            0.0474   \n",
              "372136                             0.741                            0.7508   \n",
              "372137                            0.0314                            0.0387   \n",
              "372138                             0.929                            0.8973   \n",
              "\n",
              "0                        TCGA-C5-A1MF-01                   TCGA-C5-A1BF-01  \\\n",
              "1       Cervical Squamous Cell Carcinoma  Cervical Squamous Cell Carcinoma   \n",
              "2                                 0.7018                            0.0243   \n",
              "3                                 0.0275                             0.038   \n",
              "4                                 0.0424                            0.0469   \n",
              "5                                 0.0721                            0.0713   \n",
              "...                                  ...                               ...   \n",
              "372134                            0.9804                            0.9758   \n",
              "372135                             0.065                            0.0671   \n",
              "372136                            0.7524                            0.7805   \n",
              "372137                            0.0389                            0.0353   \n",
              "372138                            0.9564                             0.927   \n",
              "\n",
              "0                        TCGA-C5-A1BK-01                   TCGA-C5-A1BI-01  \\\n",
              "1       Cervical Squamous Cell Carcinoma  Cervical Squamous Cell Carcinoma   \n",
              "2                                 0.0492                            0.0274   \n",
              "3                                 0.4205                            0.0882   \n",
              "4                                  0.438                            0.0702   \n",
              "5                                  0.194                            0.0959   \n",
              "...                                  ...                               ...   \n",
              "372134                            0.9847                            0.9843   \n",
              "372135                            0.0749                            0.0526   \n",
              "372136                            0.7938                            0.7741   \n",
              "372137                            0.0341                            0.0495   \n",
              "372138                            0.9497                            0.9291   \n",
              "\n",
              "0                           TCGA-C5-A1M9-01  \n",
              "1       Endocervical Type of Adenocarcinoma  \n",
              "2                                    0.3471  \n",
              "3                                    0.6065  \n",
              "4                                    0.0622  \n",
              "5                                    0.0665  \n",
              "...                                     ...  \n",
              "372134                                0.985  \n",
              "372135                               0.0538  \n",
              "372136                               0.6637  \n",
              "372137                               0.0362  \n",
              "372138                               0.9575  \n",
              "\n",
              "[372138 rows x 313 columns]"
            ]
          },
          "execution_count": 11,
          "metadata": {},
          "output_type": "execute_result"
        }
      ],
      "source": [
        "df.columns = df.iloc[0]\n",
        "df_new = df[1:]\n",
        "df_new"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "7434e22c",
      "metadata": {
        "id": "7434e22c",
        "outputId": "3693a59c-86a7-4584-fe95-b981d7db9d1f"
      },
      "outputs": [
        {
          "data": {
            "text/plain": [
              "Index(['SampleID', 'TCGA-EK-A3GK-01', 'TCGA-GH-A9DA-01', 'TCGA-VS-A94Y-01',\n",
              "       'TCGA-MY-A5BF-11', 'TCGA-VS-A94Z-01', 'TCGA-EA-A4BA-01',\n",
              "       'TCGA-ZJ-A8QQ-01', 'TCGA-FU-A3EO-11', 'TCGA-DG-A2KJ-01',\n",
              "       ...\n",
              "       'TCGA-C5-A1BE-01', 'TCGA-FU-A23K-01', 'TCGA-C5-A1BJ-01',\n",
              "       'TCGA-FU-A23L-01', 'TCGA-C5-A1M5-01', 'TCGA-C5-A1MF-01',\n",
              "       'TCGA-C5-A1BF-01', 'TCGA-C5-A1BK-01', 'TCGA-C5-A1BI-01',\n",
              "       'TCGA-C5-A1M9-01'],\n",
              "      dtype='object', name=0, length=313)"
            ]
          },
          "execution_count": 12,
          "metadata": {},
          "output_type": "execute_result"
        }
      ],
      "source": [
        "df_new.columns"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "ab220c6f",
      "metadata": {
        "id": "ab220c6f"
      },
      "outputs": [],
      "source": [
        "df_new2 = df_new.transpose()"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "1ea28723",
      "metadata": {
        "id": "1ea28723",
        "outputId": "8acee8f1-59a5-4de2-9171-b89e556d442c"
      },
      "outputs": [
        {
          "data": {
            "text/plain": [
              "RangeIndex(start=1, stop=372139, step=1)"
            ]
          },
          "execution_count": 14,
          "metadata": {},
          "output_type": "execute_result"
        }
      ],
      "source": [
        "df_new2.columns"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "67cecb74",
      "metadata": {
        "id": "67cecb74"
      },
      "outputs": [],
      "source": [
        "df_new2.columns = df_new2.iloc[0]\n",
        "df_new3 = df_new2[1:]"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "17ea227c",
      "metadata": {
        "id": "17ea227c",
        "outputId": "9f337811-c1bb-4845-ffcb-6f696bd71f8b"
      },
      "outputs": [
        {
          "data": {
            "text/html": [
              "<div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th>SampleID</th>\n",
              "      <th>id</th>\n",
              "      <th>histological_type</th>\n",
              "      <th>cg13332474</th>\n",
              "      <th>cg00651829</th>\n",
              "      <th>cg17027195</th>\n",
              "      <th>cg03050183</th>\n",
              "      <th>cg06819656</th>\n",
              "      <th>cg04244851</th>\n",
              "      <th>cg19669385</th>\n",
              "      <th>cg04244855</th>\n",
              "      <th>...</th>\n",
              "      <th>cg19358568</th>\n",
              "      <th>cg27295654</th>\n",
              "      <th>cg03116837</th>\n",
              "      <th>cg15678817</th>\n",
              "      <th>cg14483317</th>\n",
              "      <th>cg11692435</th>\n",
              "      <th>cg10230711</th>\n",
              "      <th>cg16651827</th>\n",
              "      <th>cg18138552</th>\n",
              "      <th>cg07883722</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>TCGA-EK-A3GK-01</td>\n",
              "      <td>Endocervical Type of Adenocarcinoma</td>\n",
              "      <td>0.0345</td>\n",
              "      <td>0.1921</td>\n",
              "      <td>0.0428</td>\n",
              "      <td>0.0753</td>\n",
              "      <td>0.8848</td>\n",
              "      <td>0.9057</td>\n",
              "      <td>0.966</td>\n",
              "      <td>0.8325</td>\n",
              "      <td>...</td>\n",
              "      <td>0.9502</td>\n",
              "      <td>0.8442</td>\n",
              "      <td>0.7589</td>\n",
              "      <td>0.7773</td>\n",
              "      <td>0.047</td>\n",
              "      <td>0.9878</td>\n",
              "      <td>0.0674</td>\n",
              "      <td>0.5374</td>\n",
              "      <td>0.0388</td>\n",
              "      <td>0.9557</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>TCGA-GH-A9DA-01</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>0.5353</td>\n",
              "      <td>0.6911</td>\n",
              "      <td>0.0741</td>\n",
              "      <td>0.065</td>\n",
              "      <td>0.9462</td>\n",
              "      <td>0.7869</td>\n",
              "      <td>0.9718</td>\n",
              "      <td>0.9351</td>\n",
              "      <td>...</td>\n",
              "      <td>0.9694</td>\n",
              "      <td>0.8985</td>\n",
              "      <td>0.4001</td>\n",
              "      <td>0.7125</td>\n",
              "      <td>0.0327</td>\n",
              "      <td>0.9861</td>\n",
              "      <td>0.061</td>\n",
              "      <td>0.784</td>\n",
              "      <td>0.0312</td>\n",
              "      <td>0.9336</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>TCGA-VS-A94Y-01</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>0.0287</td>\n",
              "      <td>0.0189</td>\n",
              "      <td>0.0403</td>\n",
              "      <td>0.0481</td>\n",
              "      <td>0.9193</td>\n",
              "      <td>0.6698</td>\n",
              "      <td>0.8886</td>\n",
              "      <td>0.9241</td>\n",
              "      <td>...</td>\n",
              "      <td>0.9066</td>\n",
              "      <td>0.8876</td>\n",
              "      <td>0.3343</td>\n",
              "      <td>0.6142</td>\n",
              "      <td>0.0838</td>\n",
              "      <td>0.9826</td>\n",
              "      <td>0.0554</td>\n",
              "      <td>0.7569</td>\n",
              "      <td>0.0229</td>\n",
              "      <td>0.9479</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>TCGA-MY-A5BF-11</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>0.0443</td>\n",
              "      <td>0.0202</td>\n",
              "      <td>0.0403</td>\n",
              "      <td>0.2139</td>\n",
              "      <td>0.906</td>\n",
              "      <td>0.8824</td>\n",
              "      <td>0.5539</td>\n",
              "      <td>0.8806</td>\n",
              "      <td>...</td>\n",
              "      <td>0.954</td>\n",
              "      <td>0.8981</td>\n",
              "      <td>0.4834</td>\n",
              "      <td>0.5039</td>\n",
              "      <td>0.0378</td>\n",
              "      <td>0.9888</td>\n",
              "      <td>0.0482</td>\n",
              "      <td>0.7441</td>\n",
              "      <td>0.027</td>\n",
              "      <td>0.9459</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>TCGA-VS-A94Z-01</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>0.0296</td>\n",
              "      <td>0.0164</td>\n",
              "      <td>0.0408</td>\n",
              "      <td>0.1028</td>\n",
              "      <td>0.9334</td>\n",
              "      <td>0.6517</td>\n",
              "      <td>0.5172</td>\n",
              "      <td>0.7533</td>\n",
              "      <td>...</td>\n",
              "      <td>0.9631</td>\n",
              "      <td>0.8472</td>\n",
              "      <td>0.8975</td>\n",
              "      <td>0.4612</td>\n",
              "      <td>0.0375</td>\n",
              "      <td>0.9841</td>\n",
              "      <td>0.0459</td>\n",
              "      <td>0.5798</td>\n",
              "      <td>0.0227</td>\n",
              "      <td>0.9462</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>307</th>\n",
              "      <td>TCGA-C5-A1MF-01</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>0.7018</td>\n",
              "      <td>0.0275</td>\n",
              "      <td>0.0424</td>\n",
              "      <td>0.0721</td>\n",
              "      <td>0.9485</td>\n",
              "      <td>0.7733</td>\n",
              "      <td>0.2163</td>\n",
              "      <td>0.9218</td>\n",
              "      <td>...</td>\n",
              "      <td>0.9506</td>\n",
              "      <td>0.9245</td>\n",
              "      <td>0.8996</td>\n",
              "      <td>0.6882</td>\n",
              "      <td>0.0554</td>\n",
              "      <td>0.9804</td>\n",
              "      <td>0.065</td>\n",
              "      <td>0.7524</td>\n",
              "      <td>0.0389</td>\n",
              "      <td>0.9564</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>308</th>\n",
              "      <td>TCGA-C5-A1BF-01</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>0.0243</td>\n",
              "      <td>0.038</td>\n",
              "      <td>0.0469</td>\n",
              "      <td>0.0713</td>\n",
              "      <td>0.8999</td>\n",
              "      <td>0.8293</td>\n",
              "      <td>0.9476</td>\n",
              "      <td>0.7271</td>\n",
              "      <td>...</td>\n",
              "      <td>0.9441</td>\n",
              "      <td>0.8944</td>\n",
              "      <td>0.7926</td>\n",
              "      <td>0.6508</td>\n",
              "      <td>0.0704</td>\n",
              "      <td>0.9758</td>\n",
              "      <td>0.0671</td>\n",
              "      <td>0.7805</td>\n",
              "      <td>0.0353</td>\n",
              "      <td>0.927</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>309</th>\n",
              "      <td>TCGA-C5-A1BK-01</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>0.0492</td>\n",
              "      <td>0.4205</td>\n",
              "      <td>0.438</td>\n",
              "      <td>0.194</td>\n",
              "      <td>0.885</td>\n",
              "      <td>0.8928</td>\n",
              "      <td>0.9604</td>\n",
              "      <td>0.9446</td>\n",
              "      <td>...</td>\n",
              "      <td>0.9366</td>\n",
              "      <td>0.8308</td>\n",
              "      <td>0.7423</td>\n",
              "      <td>0.4847</td>\n",
              "      <td>0.0378</td>\n",
              "      <td>0.9847</td>\n",
              "      <td>0.0749</td>\n",
              "      <td>0.7938</td>\n",
              "      <td>0.0341</td>\n",
              "      <td>0.9497</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>310</th>\n",
              "      <td>TCGA-C5-A1BI-01</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>0.0274</td>\n",
              "      <td>0.0882</td>\n",
              "      <td>0.0702</td>\n",
              "      <td>0.0959</td>\n",
              "      <td>0.494</td>\n",
              "      <td>0.6675</td>\n",
              "      <td>0.7613</td>\n",
              "      <td>0.7175</td>\n",
              "      <td>...</td>\n",
              "      <td>0.7844</td>\n",
              "      <td>0.9111</td>\n",
              "      <td>0.5827</td>\n",
              "      <td>0.3919</td>\n",
              "      <td>0.0518</td>\n",
              "      <td>0.9843</td>\n",
              "      <td>0.0526</td>\n",
              "      <td>0.7741</td>\n",
              "      <td>0.0495</td>\n",
              "      <td>0.9291</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>311</th>\n",
              "      <td>TCGA-C5-A1M9-01</td>\n",
              "      <td>Endocervical Type of Adenocarcinoma</td>\n",
              "      <td>0.3471</td>\n",
              "      <td>0.6065</td>\n",
              "      <td>0.0622</td>\n",
              "      <td>0.0665</td>\n",
              "      <td>0.9158</td>\n",
              "      <td>0.915</td>\n",
              "      <td>0.9704</td>\n",
              "      <td>0.9584</td>\n",
              "      <td>...</td>\n",
              "      <td>0.9571</td>\n",
              "      <td>0.9056</td>\n",
              "      <td>0.8995</td>\n",
              "      <td>0.4293</td>\n",
              "      <td>0.0505</td>\n",
              "      <td>0.985</td>\n",
              "      <td>0.0538</td>\n",
              "      <td>0.6637</td>\n",
              "      <td>0.0362</td>\n",
              "      <td>0.9575</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>312 rows × 372139 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "SampleID               id                    histological_type cg13332474  \\\n",
              "0         TCGA-EK-A3GK-01  Endocervical Type of Adenocarcinoma     0.0345   \n",
              "1         TCGA-GH-A9DA-01     Cervical Squamous Cell Carcinoma     0.5353   \n",
              "2         TCGA-VS-A94Y-01     Cervical Squamous Cell Carcinoma     0.0287   \n",
              "3         TCGA-MY-A5BF-11     Cervical Squamous Cell Carcinoma     0.0443   \n",
              "4         TCGA-VS-A94Z-01     Cervical Squamous Cell Carcinoma     0.0296   \n",
              "..                    ...                                  ...        ...   \n",
              "307       TCGA-C5-A1MF-01     Cervical Squamous Cell Carcinoma     0.7018   \n",
              "308       TCGA-C5-A1BF-01     Cervical Squamous Cell Carcinoma     0.0243   \n",
              "309       TCGA-C5-A1BK-01     Cervical Squamous Cell Carcinoma     0.0492   \n",
              "310       TCGA-C5-A1BI-01     Cervical Squamous Cell Carcinoma     0.0274   \n",
              "311       TCGA-C5-A1M9-01  Endocervical Type of Adenocarcinoma     0.3471   \n",
              "\n",
              "SampleID cg00651829 cg17027195 cg03050183 cg06819656 cg04244851 cg19669385  \\\n",
              "0            0.1921     0.0428     0.0753     0.8848     0.9057      0.966   \n",
              "1            0.6911     0.0741      0.065     0.9462     0.7869     0.9718   \n",
              "2            0.0189     0.0403     0.0481     0.9193     0.6698     0.8886   \n",
              "3            0.0202     0.0403     0.2139      0.906     0.8824     0.5539   \n",
              "4            0.0164     0.0408     0.1028     0.9334     0.6517     0.5172   \n",
              "..              ...        ...        ...        ...        ...        ...   \n",
              "307          0.0275     0.0424     0.0721     0.9485     0.7733     0.2163   \n",
              "308           0.038     0.0469     0.0713     0.8999     0.8293     0.9476   \n",
              "309          0.4205      0.438      0.194      0.885     0.8928     0.9604   \n",
              "310          0.0882     0.0702     0.0959      0.494     0.6675     0.7613   \n",
              "311          0.6065     0.0622     0.0665     0.9158      0.915     0.9704   \n",
              "\n",
              "SampleID cg04244855  ... cg19358568 cg27295654 cg03116837 cg15678817  \\\n",
              "0            0.8325  ...     0.9502     0.8442     0.7589     0.7773   \n",
              "1            0.9351  ...     0.9694     0.8985     0.4001     0.7125   \n",
              "2            0.9241  ...     0.9066     0.8876     0.3343     0.6142   \n",
              "3            0.8806  ...      0.954     0.8981     0.4834     0.5039   \n",
              "4            0.7533  ...     0.9631     0.8472     0.8975     0.4612   \n",
              "..              ...  ...        ...        ...        ...        ...   \n",
              "307          0.9218  ...     0.9506     0.9245     0.8996     0.6882   \n",
              "308          0.7271  ...     0.9441     0.8944     0.7926     0.6508   \n",
              "309          0.9446  ...     0.9366     0.8308     0.7423     0.4847   \n",
              "310          0.7175  ...     0.7844     0.9111     0.5827     0.3919   \n",
              "311          0.9584  ...     0.9571     0.9056     0.8995     0.4293   \n",
              "\n",
              "SampleID cg14483317 cg11692435 cg10230711 cg16651827 cg18138552 cg07883722  \n",
              "0             0.047     0.9878     0.0674     0.5374     0.0388     0.9557  \n",
              "1            0.0327     0.9861      0.061      0.784     0.0312     0.9336  \n",
              "2            0.0838     0.9826     0.0554     0.7569     0.0229     0.9479  \n",
              "3            0.0378     0.9888     0.0482     0.7441      0.027     0.9459  \n",
              "4            0.0375     0.9841     0.0459     0.5798     0.0227     0.9462  \n",
              "..              ...        ...        ...        ...        ...        ...  \n",
              "307          0.0554     0.9804      0.065     0.7524     0.0389     0.9564  \n",
              "308          0.0704     0.9758     0.0671     0.7805     0.0353      0.927  \n",
              "309          0.0378     0.9847     0.0749     0.7938     0.0341     0.9497  \n",
              "310          0.0518     0.9843     0.0526     0.7741     0.0495     0.9291  \n",
              "311          0.0505      0.985     0.0538     0.6637     0.0362     0.9575  \n",
              "\n",
              "[312 rows x 372139 columns]"
            ]
          },
          "execution_count": 16,
          "metadata": {},
          "output_type": "execute_result"
        }
      ],
      "source": [
        "df_new4 = df_new3.copy()\n",
        "df_new5 = df_new4.reset_index()\n",
        "df_new5 = df_new5.rename(columns={df_new5.columns[0]: 'id'})\n",
        "df_new6 = df_new5.copy()\n",
        "df_new6"
      ]
    },
    {
      "cell_type": "markdown",
      "id": "25b82bf1",
      "metadata": {
        "id": "25b82bf1"
      },
      "source": [
        "## FOR chi-square"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "1d5923ea",
      "metadata": {
        "id": "1d5923ea"
      },
      "outputs": [],
      "source": [
        "from scipy.stats import chi2_contingency\n",
        "\n",
        "df_new7 = df_new6.copy()\n",
        "\n",
        "# Calculate the chi-square test statistics and p-values for each feature\n",
        "chi2_stats = []\n",
        "p_values = []\n",
        "for feature in df_new7.columns:\n",
        "    contingency_table = pd.crosstab(df_new7[feature], df_new7['histological_type'])\n",
        "    chi2, p_value, _, _ = chi2_contingency(contingency_table)\n",
        "    chi2_stats.append(chi2)\n",
        "    p_values.append(p_value)\n",
        "\n",
        "# Create a DataFrame with the chi-square statistics and p-values\n",
        "chi2_df = pd.DataFrame({'Feature': df_new7.columns, 'Chi2_Stat': chi2_stats, 'P-Value': p_values})\n",
        "\n",
        "# Sort the DataFrame based on p-values in ascending order\n",
        "sorted_chi2_df = chi2_df.sort_values(by='P-Value', ascending=False)\n",
        "\n",
        "# Select the top 200 features based on p-values\n",
        "top_200_features = sorted_chi2_df['Feature'][:200]"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "62f49552",
      "metadata": {
        "id": "62f49552"
      },
      "outputs": [],
      "source": [
        "# # Extract the selected features from the DataFrame\n",
        "# selected_features_df = df[top_200_features]\n",
        "# selected_features_df"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "66ac31fe",
      "metadata": {
        "id": "66ac31fe",
        "outputId": "c7417c25-7f86-4868-b948-d0aae49db025"
      },
      "outputs": [
        {
          "data": {
            "text/plain": [
              "135040    cg26961332\n",
              "18098     cg01847620\n",
              "221174    cg01814098\n",
              "342393    cg17812026\n",
              "353303    cg25800170\n",
              "             ...    \n",
              "48664     cg08839858\n",
              "338636    cg15794252\n",
              "333092    cg09806118\n",
              "5688      cg04020999\n",
              "108042    cg06960784\n",
              "Name: Feature, Length: 200, dtype: object"
            ]
          },
          "execution_count": 21,
          "metadata": {},
          "output_type": "execute_result"
        }
      ],
      "source": [
        "top_200_features"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "808199d6",
      "metadata": {
        "id": "808199d6"
      },
      "outputs": [],
      "source": [
        "# Assuming your selected feature IDs are stored in a Series named 'selected_feature_ids'\n",
        "# Convert the Series to a list\n",
        "selected_feature_ids = list(top_200_features)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "c96ecf1e",
      "metadata": {
        "id": "c96ecf1e"
      },
      "outputs": [],
      "source": [
        "selected_df = top_200_features.to_frame(name='feature_id')"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "381bb429",
      "metadata": {
        "id": "381bb429",
        "outputId": "b5907d8e-888e-419c-e15d-a92237d8fff4"
      },
      "outputs": [
        {
          "data": {
            "text/html": [
              "<div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
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              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>feature_id</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>135040</th>\n",
              "      <td>cg26961332</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>18098</th>\n",
              "      <td>cg01847620</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>221174</th>\n",
              "      <td>cg01814098</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>342393</th>\n",
              "      <td>cg17812026</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>353303</th>\n",
              "      <td>cg25800170</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>48664</th>\n",
              "      <td>cg08839858</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>338636</th>\n",
              "      <td>cg15794252</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>333092</th>\n",
              "      <td>cg09806118</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5688</th>\n",
              "      <td>cg04020999</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>108042</th>\n",
              "      <td>cg06960784</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>200 rows × 1 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "        feature_id\n",
              "135040  cg26961332\n",
              "18098   cg01847620\n",
              "221174  cg01814098\n",
              "342393  cg17812026\n",
              "353303  cg25800170\n",
              "...            ...\n",
              "48664   cg08839858\n",
              "338636  cg15794252\n",
              "333092  cg09806118\n",
              "5688    cg04020999\n",
              "108042  cg06960784\n",
              "\n",
              "[200 rows x 1 columns]"
            ]
          },
          "execution_count": 28,
          "metadata": {},
          "output_type": "execute_result"
        }
      ],
      "source": [
        "selected_df"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "47ad3490",
      "metadata": {
        "id": "47ad3490",
        "outputId": "9f9f7ef7-a924-4aa6-9729-75b996e2cfef"
      },
      "outputs": [
        {
          "data": {
            "text/plain": [
              "Index(['id', 'histological_type', 'cg13332474', 'cg00651829', 'cg17027195',\n",
              "       'cg03050183', 'cg06819656', 'cg04244851', 'cg19669385', 'cg04244855',\n",
              "       ...\n",
              "       'cg19358568', 'cg27295654', 'cg03116837', 'cg15678817', 'cg14483317',\n",
              "       'cg11692435', 'cg10230711', 'cg16651827', 'cg18138552', 'cg07883722'],\n",
              "      dtype='object', name='SampleID', length=372139)"
            ]
          },
          "execution_count": 35,
          "metadata": {},
          "output_type": "execute_result"
        }
      ],
      "source": [
        "df_new7.columns"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "ac55150e",
      "metadata": {
        "id": "ac55150e"
      },
      "outputs": [],
      "source": [
        "filtered_dataset = df_new7[['id', 'histological_type'] + selected_df['feature_id'].tolist()]"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "944323a4",
      "metadata": {
        "id": "944323a4",
        "outputId": "1bc03936-6a91-44a7-82ea-a17b714bd610"
      },
      "outputs": [
        {
          "data": {
            "text/html": [
              "<div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
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              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th>SampleID</th>\n",
              "      <th>id</th>\n",
              "      <th>histological_type</th>\n",
              "      <th>cg26961332</th>\n",
              "      <th>cg01847620</th>\n",
              "      <th>cg01814098</th>\n",
              "      <th>cg17812026</th>\n",
              "      <th>cg25800170</th>\n",
              "      <th>cg13682477</th>\n",
              "      <th>cg23889391</th>\n",
              "      <th>cg26082557</th>\n",
              "      <th>...</th>\n",
              "      <th>cg08643007</th>\n",
              "      <th>cg08367083</th>\n",
              "      <th>cg00810836</th>\n",
              "      <th>cg04087237</th>\n",
              "      <th>cg25379026</th>\n",
              "      <th>cg08839858</th>\n",
              "      <th>cg15794252</th>\n",
              "      <th>cg09806118</th>\n",
              "      <th>cg04020999</th>\n",
              "      <th>cg06960784</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>TCGA-EK-A3GK-01</td>\n",
              "      <td>Endocervical Type of Adenocarcinoma</td>\n",
              "      <td>0.9904</td>\n",
              "      <td>0.986</td>\n",
              "      <td>0.0247</td>\n",
              "      <td>0.957</td>\n",
              "      <td>0.0166</td>\n",
              "      <td>0.0166</td>\n",
              "      <td>0.0158</td>\n",
              "      <td>0.016</td>\n",
              "      <td>...</td>\n",
              "      <td>0.0317</td>\n",
              "      <td>0.0183</td>\n",
              "      <td>0.0621</td>\n",
              "      <td>0.0652</td>\n",
              "      <td>0.0122</td>\n",
              "      <td>0.0224</td>\n",
              "      <td>0.0124</td>\n",
              "      <td>0.012</td>\n",
              "      <td>0.9778</td>\n",
              "      <td>0.0128</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>TCGA-GH-A9DA-01</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>0.991</td>\n",
              "      <td>0.9909</td>\n",
              "      <td>0.015</td>\n",
              "      <td>0.9914</td>\n",
              "      <td>0.0139</td>\n",
              "      <td>0.0172</td>\n",
              "      <td>0.6539</td>\n",
              "      <td>0.0113</td>\n",
              "      <td>...</td>\n",
              "      <td>0.0377</td>\n",
              "      <td>0.0147</td>\n",
              "      <td>0.017</td>\n",
              "      <td>0.0191</td>\n",
              "      <td>0.0162</td>\n",
              "      <td>0.6017</td>\n",
              "      <td>0.0623</td>\n",
              "      <td>0.4581</td>\n",
              "      <td>0.9914</td>\n",
              "      <td>0.3205</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>TCGA-VS-A94Y-01</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>0.9883</td>\n",
              "      <td>0.9424</td>\n",
              "      <td>0.0174</td>\n",
              "      <td>0.9776</td>\n",
              "      <td>0.2976</td>\n",
              "      <td>0.6157</td>\n",
              "      <td>0.0132</td>\n",
              "      <td>0.0454</td>\n",
              "      <td>...</td>\n",
              "      <td>0.0257</td>\n",
              "      <td>0.0224</td>\n",
              "      <td>0.019</td>\n",
              "      <td>0.0687</td>\n",
              "      <td>0.4693</td>\n",
              "      <td>0.5097</td>\n",
              "      <td>0.0144</td>\n",
              "      <td>0.0115</td>\n",
              "      <td>0.9845</td>\n",
              "      <td>0.0163</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>TCGA-MY-A5BF-11</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>0.9901</td>\n",
              "      <td>0.9858</td>\n",
              "      <td>0.0174</td>\n",
              "      <td>0.9898</td>\n",
              "      <td>0.0137</td>\n",
              "      <td>0.0211</td>\n",
              "      <td>0.0169</td>\n",
              "      <td>0.0147</td>\n",
              "      <td>...</td>\n",
              "      <td>0.0208</td>\n",
              "      <td>0.0264</td>\n",
              "      <td>0.0267</td>\n",
              "      <td>0.0112</td>\n",
              "      <td>0.0208</td>\n",
              "      <td>0.0193</td>\n",
              "      <td>0.0158</td>\n",
              "      <td>0.0144</td>\n",
              "      <td>0.986</td>\n",
              "      <td>0.0212</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>TCGA-VS-A94Z-01</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>0.8803</td>\n",
              "      <td>0.6852</td>\n",
              "      <td>0.0172</td>\n",
              "      <td>0.567</td>\n",
              "      <td>0.2188</td>\n",
              "      <td>0.5187</td>\n",
              "      <td>0.4858</td>\n",
              "      <td>0.4888</td>\n",
              "      <td>...</td>\n",
              "      <td>0.0282</td>\n",
              "      <td>0.2056</td>\n",
              "      <td>0.0174</td>\n",
              "      <td>0.0142</td>\n",
              "      <td>0.5561</td>\n",
              "      <td>0.419</td>\n",
              "      <td>0.0168</td>\n",
              "      <td>0.0121</td>\n",
              "      <td>0.9844</td>\n",
              "      <td>0.0603</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>307</th>\n",
              "      <td>TCGA-C5-A1MF-01</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>0.987</td>\n",
              "      <td>0.9878</td>\n",
              "      <td>0.0217</td>\n",
              "      <td>0.7349</td>\n",
              "      <td>0.018</td>\n",
              "      <td>0.0252</td>\n",
              "      <td>0.0168</td>\n",
              "      <td>0.6354</td>\n",
              "      <td>...</td>\n",
              "      <td>0.0292</td>\n",
              "      <td>0.034</td>\n",
              "      <td>0.0227</td>\n",
              "      <td>0.0179</td>\n",
              "      <td>0.3376</td>\n",
              "      <td>0.0217</td>\n",
              "      <td>0.015</td>\n",
              "      <td>0.0149</td>\n",
              "      <td>0.981</td>\n",
              "      <td>0.0186</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>308</th>\n",
              "      <td>TCGA-C5-A1BF-01</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>0.9801</td>\n",
              "      <td>0.9022</td>\n",
              "      <td>0.0208</td>\n",
              "      <td>0.9823</td>\n",
              "      <td>0.019</td>\n",
              "      <td>0.0239</td>\n",
              "      <td>0.0146</td>\n",
              "      <td>0.014</td>\n",
              "      <td>...</td>\n",
              "      <td>0.0362</td>\n",
              "      <td>0.0259</td>\n",
              "      <td>0.0416</td>\n",
              "      <td>0.0232</td>\n",
              "      <td>0.0197</td>\n",
              "      <td>0.536</td>\n",
              "      <td>0.0134</td>\n",
              "      <td>0.41</td>\n",
              "      <td>0.9786</td>\n",
              "      <td>0.0184</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>309</th>\n",
              "      <td>TCGA-C5-A1BK-01</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>0.9879</td>\n",
              "      <td>0.6833</td>\n",
              "      <td>0.1408</td>\n",
              "      <td>0.8738</td>\n",
              "      <td>0.0223</td>\n",
              "      <td>0.4855</td>\n",
              "      <td>0.1336</td>\n",
              "      <td>0.5528</td>\n",
              "      <td>...</td>\n",
              "      <td>0.0244</td>\n",
              "      <td>0.0297</td>\n",
              "      <td>0.0349</td>\n",
              "      <td>0.1042</td>\n",
              "      <td>0.0997</td>\n",
              "      <td>0.228</td>\n",
              "      <td>0.2108</td>\n",
              "      <td>0.3921</td>\n",
              "      <td>0.9809</td>\n",
              "      <td>0.5083</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>310</th>\n",
              "      <td>TCGA-C5-A1BI-01</td>\n",
              "      <td>Cervical Squamous Cell Carcinoma</td>\n",
              "      <td>0.9434</td>\n",
              "      <td>0.9259</td>\n",
              "      <td>0.0244</td>\n",
              "      <td>0.7724</td>\n",
              "      <td>0.2028</td>\n",
              "      <td>0.035</td>\n",
              "      <td>0.4781</td>\n",
              "      <td>0.0268</td>\n",
              "      <td>...</td>\n",
              "      <td>0.0463</td>\n",
              "      <td>0.0372</td>\n",
              "      <td>0.1238</td>\n",
              "      <td>0.0198</td>\n",
              "      <td>0.5899</td>\n",
              "      <td>0.3088</td>\n",
              "      <td>0.2795</td>\n",
              "      <td>0.0145</td>\n",
              "      <td>0.9673</td>\n",
              "      <td>0.0293</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>311</th>\n",
              "      <td>TCGA-C5-A1M9-01</td>\n",
              "      <td>Endocervical Type of Adenocarcinoma</td>\n",
              "      <td>0.9896</td>\n",
              "      <td>0.9833</td>\n",
              "      <td>0.0207</td>\n",
              "      <td>0.9896</td>\n",
              "      <td>0.0278</td>\n",
              "      <td>0.0202</td>\n",
              "      <td>0.0149</td>\n",
              "      <td>0.0159</td>\n",
              "      <td>...</td>\n",
              "      <td>0.0285</td>\n",
              "      <td>0.0168</td>\n",
              "      <td>0.0329</td>\n",
              "      <td>0.3369</td>\n",
              "      <td>0.0174</td>\n",
              "      <td>0.0167</td>\n",
              "      <td>0.0177</td>\n",
              "      <td>0.0143</td>\n",
              "      <td>0.9846</td>\n",
              "      <td>0.3213</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>312 rows × 202 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "SampleID               id                    histological_type cg26961332  \\\n",
              "0         TCGA-EK-A3GK-01  Endocervical Type of Adenocarcinoma     0.9904   \n",
              "1         TCGA-GH-A9DA-01     Cervical Squamous Cell Carcinoma      0.991   \n",
              "2         TCGA-VS-A94Y-01     Cervical Squamous Cell Carcinoma     0.9883   \n",
              "3         TCGA-MY-A5BF-11     Cervical Squamous Cell Carcinoma     0.9901   \n",
              "4         TCGA-VS-A94Z-01     Cervical Squamous Cell Carcinoma     0.8803   \n",
              "..                    ...                                  ...        ...   \n",
              "307       TCGA-C5-A1MF-01     Cervical Squamous Cell Carcinoma      0.987   \n",
              "308       TCGA-C5-A1BF-01     Cervical Squamous Cell Carcinoma     0.9801   \n",
              "309       TCGA-C5-A1BK-01     Cervical Squamous Cell Carcinoma     0.9879   \n",
              "310       TCGA-C5-A1BI-01     Cervical Squamous Cell Carcinoma     0.9434   \n",
              "311       TCGA-C5-A1M9-01  Endocervical Type of Adenocarcinoma     0.9896   \n",
              "\n",
              "SampleID cg01847620 cg01814098 cg17812026 cg25800170 cg13682477 cg23889391  \\\n",
              "0             0.986     0.0247      0.957     0.0166     0.0166     0.0158   \n",
              "1            0.9909      0.015     0.9914     0.0139     0.0172     0.6539   \n",
              "2            0.9424     0.0174     0.9776     0.2976     0.6157     0.0132   \n",
              "3            0.9858     0.0174     0.9898     0.0137     0.0211     0.0169   \n",
              "4            0.6852     0.0172      0.567     0.2188     0.5187     0.4858   \n",
              "..              ...        ...        ...        ...        ...        ...   \n",
              "307          0.9878     0.0217     0.7349      0.018     0.0252     0.0168   \n",
              "308          0.9022     0.0208     0.9823      0.019     0.0239     0.0146   \n",
              "309          0.6833     0.1408     0.8738     0.0223     0.4855     0.1336   \n",
              "310          0.9259     0.0244     0.7724     0.2028      0.035     0.4781   \n",
              "311          0.9833     0.0207     0.9896     0.0278     0.0202     0.0149   \n",
              "\n",
              "SampleID cg26082557  ... cg08643007 cg08367083 cg00810836 cg04087237  \\\n",
              "0             0.016  ...     0.0317     0.0183     0.0621     0.0652   \n",
              "1            0.0113  ...     0.0377     0.0147      0.017     0.0191   \n",
              "2            0.0454  ...     0.0257     0.0224      0.019     0.0687   \n",
              "3            0.0147  ...     0.0208     0.0264     0.0267     0.0112   \n",
              "4            0.4888  ...     0.0282     0.2056     0.0174     0.0142   \n",
              "..              ...  ...        ...        ...        ...        ...   \n",
              "307          0.6354  ...     0.0292      0.034     0.0227     0.0179   \n",
              "308           0.014  ...     0.0362     0.0259     0.0416     0.0232   \n",
              "309          0.5528  ...     0.0244     0.0297     0.0349     0.1042   \n",
              "310          0.0268  ...     0.0463     0.0372     0.1238     0.0198   \n",
              "311          0.0159  ...     0.0285     0.0168     0.0329     0.3369   \n",
              "\n",
              "SampleID cg25379026 cg08839858 cg15794252 cg09806118 cg04020999 cg06960784  \n",
              "0            0.0122     0.0224     0.0124      0.012     0.9778     0.0128  \n",
              "1            0.0162     0.6017     0.0623     0.4581     0.9914     0.3205  \n",
              "2            0.4693     0.5097     0.0144     0.0115     0.9845     0.0163  \n",
              "3            0.0208     0.0193     0.0158     0.0144      0.986     0.0212  \n",
              "4            0.5561      0.419     0.0168     0.0121     0.9844     0.0603  \n",
              "..              ...        ...        ...        ...        ...        ...  \n",
              "307          0.3376     0.0217      0.015     0.0149      0.981     0.0186  \n",
              "308          0.0197      0.536     0.0134       0.41     0.9786     0.0184  \n",
              "309          0.0997      0.228     0.2108     0.3921     0.9809     0.5083  \n",
              "310          0.5899     0.3088     0.2795     0.0145     0.9673     0.0293  \n",
              "311          0.0174     0.0167     0.0177     0.0143     0.9846     0.3213  \n",
              "\n",
              "[312 rows x 202 columns]"
            ]
          },
          "execution_count": 43,
          "metadata": {},
          "output_type": "execute_result"
        }
      ],
      "source": [
        "filtered_dataset"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "217321d4",
      "metadata": {
        "id": "217321d4"
      },
      "outputs": [],
      "source": [
        "filtered_dataset.to_csv('Downloads/filtered_dataset.csv', index=False)"
      ]
    }
  ],
  "metadata": {
    "kernelspec": {
      "display_name": "Python 3 (ipykernel)",
      "language": "python",
      "name": "python3"
    },
    "language_info": {
      "codemirror_mode": {
        "name": "ipython",
        "version": 3
      },
      "file_extension": ".py",
      "mimetype": "text/x-python",
      "name": "python",
      "nbconvert_exporter": "python",
      "pygments_lexer": "ipython3",
      "version": "3.9.13"
    },
    "colab": {
      "provenance": [],
      "include_colab_link": true
    }
  },
  "nbformat": 4,
  "nbformat_minor": 5
}