test.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "b15e0cd9-bcec-47ca-b095-326d208de825",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.1.0\n"
     ]
    }
   ],
   "source": [
    "import dysregnet\n",
    "import importlib.metadata\n",
    "print(importlib.metadata.version('dysregnet'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "eb0a601a-632c-4abc-88d2-6be5d218b8ab",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "\n",
    "meta = pd.read_csv(\"test dataset/clinical.csv\")\n",
    "case = pd.read_csv(\"test dataset/expr_case.csv\" )\n",
    "control = pd.read_csv(\"test dataset/expr_control.csv\")\n",
    "grn=pd.read_csv(\"test dataset/HTRIdb_data.csv\", sep = \";\")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "ebebb019-4a9e-41d0-82ff-720806582d1d",
   "metadata": {},
   "outputs": [],
   "source": [
    "grn = grn[[\"SYMBOL_TF\",\"SYMBOL_TG\"]]\n",
    "expr=pd.concat([control,case])\n",
    "i=list(expr.iloc[:,0])\n",
    "meta=meta[ meta.iloc[:,0].isin(i)]\n",
    "meta.sample_type=meta.sample_type.apply(lambda x: 0 if x=='Solid Tissue Normal' else 1)\n",
    "meta[\"birth_days_to\"] = meta[\"birth_days_to\"].fillna(meta[\"birth_days_to\"].mean())\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "adfea7e9-5378-4605-9493-2879b709c2b6",
   "metadata": {},
   "source": [
    "# Expression table "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "4fec75f2-2aa7-4d38-acba-022fdf31dcc8",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "\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>Unnamed: 0</th>\n",
       "      <th>SNAP29</th>\n",
       "      <th>CENPP</th>\n",
       "      <th>DHX8</th>\n",
       "      <th>EFNA5</th>\n",
       "      <th>SORCS1</th>\n",
       "      <th>CTSL</th>\n",
       "      <th>CALB1</th>\n",
       "      <th>PCDHA2</th>\n",
       "      <th>PSMC3IP</th>\n",
       "      <th>...</th>\n",
       "      <th>ATF7-NPFF</th>\n",
       "      <th>ARHGEF35</th>\n",
       "      <th>LGALS7B</th>\n",
       "      <th>NECAB3</th>\n",
       "      <th>ENDOG</th>\n",
       "      <th>CCDC74A</th>\n",
       "      <th>PODNL1</th>\n",
       "      <th>SDCBP</th>\n",
       "      <th>GEN1</th>\n",
       "      <th>MORN1</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>TCGA-BH-A0DL-11</td>\n",
       "      <td>0.011039</td>\n",
       "      <td>-0.433531</td>\n",
       "      <td>0.148784</td>\n",
       "      <td>0.881892</td>\n",
       "      <td>0.397204</td>\n",
       "      <td>0.291111</td>\n",
       "      <td>0.202938</td>\n",
       "      <td>0.830075</td>\n",
       "      <td>-0.660478</td>\n",
       "      <td>...</td>\n",
       "      <td>2.107643</td>\n",
       "      <td>-0.210640</td>\n",
       "      <td>1.364119</td>\n",
       "      <td>-1.194724</td>\n",
       "      <td>-0.340685</td>\n",
       "      <td>-0.441246</td>\n",
       "      <td>0.029741</td>\n",
       "      <td>0.821344</td>\n",
       "      <td>0.556907</td>\n",
       "      <td>0.357661</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>TCGA-BH-A0BQ-11</td>\n",
       "      <td>-0.396226</td>\n",
       "      <td>-1.101919</td>\n",
       "      <td>0.125927</td>\n",
       "      <td>1.076358</td>\n",
       "      <td>1.130668</td>\n",
       "      <td>-0.994074</td>\n",
       "      <td>1.458626</td>\n",
       "      <td>0.596539</td>\n",
       "      <td>-1.280311</td>\n",
       "      <td>...</td>\n",
       "      <td>0.954723</td>\n",
       "      <td>0.630559</td>\n",
       "      <td>1.248929</td>\n",
       "      <td>-1.249310</td>\n",
       "      <td>-0.220519</td>\n",
       "      <td>-0.123971</td>\n",
       "      <td>1.129753</td>\n",
       "      <td>0.316649</td>\n",
       "      <td>0.489605</td>\n",
       "      <td>0.182808</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>TCGA-BH-A18J-11</td>\n",
       "      <td>-0.289872</td>\n",
       "      <td>-0.875374</td>\n",
       "      <td>0.084214</td>\n",
       "      <td>0.595231</td>\n",
       "      <td>-0.138605</td>\n",
       "      <td>0.214701</td>\n",
       "      <td>1.554930</td>\n",
       "      <td>-0.567784</td>\n",
       "      <td>-0.867467</td>\n",
       "      <td>...</td>\n",
       "      <td>1.975898</td>\n",
       "      <td>0.727769</td>\n",
       "      <td>1.129948</td>\n",
       "      <td>-0.634645</td>\n",
       "      <td>-0.892021</td>\n",
       "      <td>-0.807988</td>\n",
       "      <td>0.204867</td>\n",
       "      <td>0.702972</td>\n",
       "      <td>-0.128616</td>\n",
       "      <td>0.410850</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>TCGA-BH-A18R-11</td>\n",
       "      <td>-0.367729</td>\n",
       "      <td>-0.845867</td>\n",
       "      <td>-0.890999</td>\n",
       "      <td>0.537888</td>\n",
       "      <td>0.340662</td>\n",
       "      <td>-0.389748</td>\n",
       "      <td>0.073558</td>\n",
       "      <td>0.264370</td>\n",
       "      <td>-0.664225</td>\n",
       "      <td>...</td>\n",
       "      <td>0.922040</td>\n",
       "      <td>0.333581</td>\n",
       "      <td>0.341515</td>\n",
       "      <td>-0.985415</td>\n",
       "      <td>-0.816454</td>\n",
       "      <td>-0.518450</td>\n",
       "      <td>-0.521705</td>\n",
       "      <td>0.189719</td>\n",
       "      <td>-1.269150</td>\n",
       "      <td>0.043587</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>4 rows × 18908 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        Unnamed: 0    SNAP29     CENPP      DHX8     EFNA5    SORCS1  \\\n",
       "0  TCGA-BH-A0DL-11  0.011039 -0.433531  0.148784  0.881892  0.397204   \n",
       "1  TCGA-BH-A0BQ-11 -0.396226 -1.101919  0.125927  1.076358  1.130668   \n",
       "2  TCGA-BH-A18J-11 -0.289872 -0.875374  0.084214  0.595231 -0.138605   \n",
       "3  TCGA-BH-A18R-11 -0.367729 -0.845867 -0.890999  0.537888  0.340662   \n",
       "\n",
       "       CTSL     CALB1    PCDHA2   PSMC3IP  ...  ATF7-NPFF  ARHGEF35   LGALS7B  \\\n",
       "0  0.291111  0.202938  0.830075 -0.660478  ...   2.107643 -0.210640  1.364119   \n",
       "1 -0.994074  1.458626  0.596539 -1.280311  ...   0.954723  0.630559  1.248929   \n",
       "2  0.214701  1.554930 -0.567784 -0.867467  ...   1.975898  0.727769  1.129948   \n",
       "3 -0.389748  0.073558  0.264370 -0.664225  ...   0.922040  0.333581  0.341515   \n",
       "\n",
       "     NECAB3     ENDOG   CCDC74A    PODNL1     SDCBP      GEN1     MORN1  \n",
       "0 -1.194724 -0.340685 -0.441246  0.029741  0.821344  0.556907  0.357661  \n",
       "1 -1.249310 -0.220519 -0.123971  1.129753  0.316649  0.489605  0.182808  \n",
       "2 -0.634645 -0.892021 -0.807988  0.204867  0.702972 -0.128616  0.410850  \n",
       "3 -0.985415 -0.816454 -0.518450 -0.521705  0.189719 -1.269150  0.043587  \n",
       "\n",
       "[4 rows x 18908 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "expr.head(4)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f1f275f6-ef96-4e1b-a37b-8bb96585395d",
   "metadata": {},
   "source": [
    "# Meta table \n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "143700c2-33b4-43a7-8091-fda17d57093b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "    }\n",
       "\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>sample</th>\n",
       "      <th>_PATIENT</th>\n",
       "      <th>cancer type abbreviation</th>\n",
       "      <th>age_at_initial_pathologic_diagnosis</th>\n",
       "      <th>gender</th>\n",
       "      <th>race</th>\n",
       "      <th>ajcc_pathologic_tumor_stage</th>\n",
       "      <th>clinical_stage</th>\n",
       "      <th>histological_type</th>\n",
       "      <th>histological_grade</th>\n",
       "      <th>...</th>\n",
       "      <th>DSS</th>\n",
       "      <th>DSS.time</th>\n",
       "      <th>DFI</th>\n",
       "      <th>DFI.time</th>\n",
       "      <th>PFI</th>\n",
       "      <th>PFI.time</th>\n",
       "      <th>Redaction</th>\n",
       "      <th>sample_type_id</th>\n",
       "      <th>sample_type</th>\n",
       "      <th>_primary_disease</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>TCGA-3C-AAAU-01</td>\n",
       "      <td>TCGA-3C-AAAU</td>\n",
       "      <td>BRCA</td>\n",
       "      <td>55.0</td>\n",
       "      <td>FEMALE</td>\n",
       "      <td>WHITE</td>\n",
       "      <td>Stage X</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Infiltrating Lobular Carcinoma</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4047.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1808.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1808.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1</td>\n",
       "      <td>breast invasive carcinoma</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>TCGA-3C-AALI-01</td>\n",
       "      <td>TCGA-3C-AALI</td>\n",
       "      <td>BRCA</td>\n",
       "      <td>50.0</td>\n",
       "      <td>FEMALE</td>\n",
       "      <td>BLACK OR AFRICAN AMERICAN</td>\n",
       "      <td>Stage IIB</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Infiltrating Ductal Carcinoma</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4005.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4005.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4005.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1</td>\n",
       "      <td>breast invasive carcinoma</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>TCGA-3C-AALJ-01</td>\n",
       "      <td>TCGA-3C-AALJ</td>\n",
       "      <td>BRCA</td>\n",
       "      <td>62.0</td>\n",
       "      <td>FEMALE</td>\n",
       "      <td>BLACK OR AFRICAN AMERICAN</td>\n",
       "      <td>Stage IIB</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Infiltrating Ductal Carcinoma</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1474.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1474.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1474.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1</td>\n",
       "      <td>breast invasive carcinoma</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>TCGA-3C-AALK-01</td>\n",
       "      <td>TCGA-3C-AALK</td>\n",
       "      <td>BRCA</td>\n",
       "      <td>52.0</td>\n",
       "      <td>FEMALE</td>\n",
       "      <td>BLACK OR AFRICAN AMERICAN</td>\n",
       "      <td>Stage IA</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Infiltrating Ductal Carcinoma</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1448.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1448.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1</td>\n",
       "      <td>breast invasive carcinoma</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>4 rows × 37 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            sample      _PATIENT cancer type abbreviation  \\\n",
       "0  TCGA-3C-AAAU-01  TCGA-3C-AAAU                     BRCA   \n",
       "1  TCGA-3C-AALI-01  TCGA-3C-AALI                     BRCA   \n",
       "2  TCGA-3C-AALJ-01  TCGA-3C-AALJ                     BRCA   \n",
       "3  TCGA-3C-AALK-01  TCGA-3C-AALK                     BRCA   \n",
       "\n",
       "   age_at_initial_pathologic_diagnosis  gender                       race  \\\n",
       "0                                 55.0  FEMALE                      WHITE   \n",
       "1                                 50.0  FEMALE  BLACK OR AFRICAN AMERICAN   \n",
       "2                                 62.0  FEMALE  BLACK OR AFRICAN AMERICAN   \n",
       "3                                 52.0  FEMALE  BLACK OR AFRICAN AMERICAN   \n",
       "\n",
       "  ajcc_pathologic_tumor_stage clinical_stage               histological_type  \\\n",
       "0                     Stage X            NaN  Infiltrating Lobular Carcinoma   \n",
       "1                   Stage IIB            NaN   Infiltrating Ductal Carcinoma   \n",
       "2                   Stage IIB            NaN   Infiltrating Ductal Carcinoma   \n",
       "3                    Stage IA            NaN   Infiltrating Ductal Carcinoma   \n",
       "\n",
       "  histological_grade  ...  DSS DSS.time  DFI DFI.time  PFI  PFI.time  \\\n",
       "0                NaN  ...  0.0   4047.0  1.0   1808.0  1.0    1808.0   \n",
       "1                NaN  ...  0.0   4005.0  0.0   4005.0  0.0    4005.0   \n",
       "2                NaN  ...  0.0   1474.0  0.0   1474.0  0.0    1474.0   \n",
       "3                NaN  ...  0.0   1448.0  NaN      NaN  0.0    1448.0   \n",
       "\n",
       "   Redaction sample_type_id sample_type           _primary_disease  \n",
       "0        NaN            1.0           1  breast invasive carcinoma  \n",
       "1        NaN            1.0           1  breast invasive carcinoma  \n",
       "2        NaN            1.0           1  breast invasive carcinoma  \n",
       "3        NaN            1.0           1  breast invasive carcinoma  \n",
       "\n",
       "[4 rows x 37 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "meta.head(4)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "09e307f0-80d5-49d2-8725-081acfe90813",
   "metadata": {},
   "source": [
    "# GRN table"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "5c4773ff-7f02-410f-8ff2-f5aa02ad98f2",
   "metadata": {},
   "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></th>\n",
       "      <th>SYMBOL_TF</th>\n",
       "      <th>SYMBOL_TG</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>PARP1</td>\n",
       "      <td>BRCA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>PARP1</td>\n",
       "      <td>BRCA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AHR</td>\n",
       "      <td>CYP1A1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AHR</td>\n",
       "      <td>CYP1A1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  SYMBOL_TF SYMBOL_TG\n",
       "0     PARP1     BRCA2\n",
       "1     PARP1     BRCA2\n",
       "2       AHR    CYP1A1\n",
       "3       AHR    CYP1A1"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "grn.head(4)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3ce91691-82a1-48c7-be6e-4e3c43b6fd86",
   "metadata": {},
   "source": [
    "# Define the design matrix from the meta table\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "1244cf2e-396f-4cc9-9532-bf134b92f8e1",
   "metadata": {},
   "outputs": [],
   "source": [
    "CatCov=['race','gender']  \n",
    "ConCov=['birth_days_to',]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1efc97dc-803c-468c-8301-309bfcf2e443",
   "metadata": {},
   "source": [
    "# Run DysRegNet\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "43ac057e-9d32-4a39-892a-0b728906e68f",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "14162it [00:46, 304.82it/s]\n"
     ]
    }
   ],
   "source": [
    "data=dysregnet.run(expression_data=expr,\n",
    "                   meta=meta, \n",
    "                   CatCov=CatCov,\n",
    "                   ConCov=ConCov,\n",
    "                   GRN=grn,\n",
    "                   normaltest=True,\n",
    "                   R2_threshold=.2,\n",
    "                   conCol='sample_type')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a218bc6f-186a-47db-85d4-50cd5cee3c8c",
   "metadata": {},
   "source": [
    "# Results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "b8791d43-05eb-4f64-a8aa-a7e2be784da5",
   "metadata": {},
   "outputs": [
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>(PARP1, BRCA2)</th>\n",
       "      <th>(AHR, CYP1B1)</th>\n",
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       "      <th>...</th>\n",
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       "      <th>(THAP7, CDKN2A)</th>\n",
       "      <th>(FOXP2, PLAUR)</th>\n",
       "      <th>(FOXP2, CNTNAP2)</th>\n",
       "      <th>(ZNF653, CDKN2A)</th>\n",
       "      <th>(E2F7, SP1)</th>\n",
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       "      <th>(ZNF384, CDKN2A)</th>\n",
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      "text/plain": [
       "                 (PARP1, BRCA2)  (AHR, CYP1B1)  (AHR, FOS)  (AHR, SOS1)  \\\n",
       "patient id                                                                \n",
       "TCGA-3C-AAAU-01             0.0            0.0         0.0          0.0   \n",
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       "TCGA-4H-AAAK-01             0.0            0.0         0.0          0.0   \n",
       "...                         ...            ...         ...          ...   \n",
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       "TCGA-Z7-A8R6-01             0.0            0.0         0.0          0.0   \n",
       "\n",
       "                 (AHR, UGT1A6)  (AR, ABCA1)  (AR, ABCA2)  (AR, ABCF1)  \\\n",
       "patient id                                                              \n",
       "TCGA-3C-AAAU-01            0.0          0.0          0.0          0.0   \n",
       "TCGA-3C-AALI-01            0.0          0.0          0.0          0.0   \n",
       "TCGA-3C-AALJ-01            0.0          0.0          0.0          0.0   \n",
       "TCGA-3C-AALK-01            0.0          0.0          0.0          0.0   \n",
       "TCGA-4H-AAAK-01            0.0          0.0          0.0          0.0   \n",
       "...                        ...          ...          ...          ...   \n",
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       "TCGA-XX-A899-01            0.0          0.0          0.0          0.0   \n",
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       "TCGA-Z7-A8R6-01            0.0          0.0          0.0          0.0   \n",
       "\n",
       "                 (AR, ABCA4)  (AR, ABL1)  ...  (ZNF419, CDKN2A)  \\\n",
       "patient id                                ...                     \n",
       "TCGA-3C-AAAU-01          0.0         0.0  ...               0.0   \n",
       "TCGA-3C-AALI-01          0.0         0.0  ...               0.0   \n",
       "TCGA-3C-AALJ-01          0.0         0.0  ...               0.0   \n",
       "TCGA-3C-AALK-01          0.0         0.0  ...               0.0   \n",
       "TCGA-4H-AAAK-01          0.0         0.0  ...               0.0   \n",
       "...                      ...         ...  ...               ...   \n",
       "TCGA-WT-AB44-01          0.0         0.0  ...               0.0   \n",
       "TCGA-XX-A899-01          0.0         0.0  ...               0.0   \n",
       "TCGA-XX-A89A-01          0.0         0.0  ...               0.0   \n",
       "TCGA-Z7-A8R5-01          0.0         0.0  ...               0.0   \n",
       "TCGA-Z7-A8R6-01          0.0         0.0  ...               0.0   \n",
       "\n",
       "                 (ZNF671, CDKN2A)  (THAP7, CDKN2A)  (FOXP2, PLAUR)  \\\n",
       "patient id                                                           \n",
       "TCGA-3C-AAAU-01               0.0              0.0             0.0   \n",
       "TCGA-3C-AALI-01               0.0              0.0             0.0   \n",
       "TCGA-3C-AALJ-01               0.0              0.0             0.0   \n",
       "TCGA-3C-AALK-01               0.0              0.0             0.0   \n",
       "TCGA-4H-AAAK-01               0.0              0.0             0.0   \n",
       "...                           ...              ...             ...   \n",
       "TCGA-WT-AB44-01               0.0              0.0             0.0   \n",
       "TCGA-XX-A899-01               0.0              0.0             0.0   \n",
       "TCGA-XX-A89A-01               0.0              0.0             0.0   \n",
       "TCGA-Z7-A8R5-01               0.0              0.0             0.0   \n",
       "TCGA-Z7-A8R6-01               0.0              0.0             0.0   \n",
       "\n",
       "                 (FOXP2, CNTNAP2)  (ZNF653, CDKN2A)  (E2F7, SP1)  \\\n",
       "patient id                                                         \n",
       "TCGA-3C-AAAU-01               0.0               0.0          0.0   \n",
       "TCGA-3C-AALI-01               0.0               0.0          0.0   \n",
       "TCGA-3C-AALJ-01               0.0               0.0          0.0   \n",
       "TCGA-3C-AALK-01               0.0               0.0          0.0   \n",
       "TCGA-4H-AAAK-01               0.0               0.0          0.0   \n",
       "...                           ...               ...          ...   \n",
       "TCGA-WT-AB44-01               0.0               0.0          0.0   \n",
       "TCGA-XX-A899-01               0.0               0.0          0.0   \n",
       "TCGA-XX-A89A-01               0.0               0.0          0.0   \n",
       "TCGA-Z7-A8R5-01               0.0               0.0          0.0   \n",
       "TCGA-Z7-A8R6-01               0.0               0.0          0.0   \n",
       "\n",
       "                 (ZNF417, CDKN2A)  (ZNF384, CDKN2A)  (ZNF384, COL1A1)  \n",
       "patient id                                                             \n",
       "TCGA-3C-AAAU-01               0.0               0.0               0.0  \n",
       "TCGA-3C-AALI-01               0.0               0.0               0.0  \n",
       "TCGA-3C-AALJ-01               0.0               0.0               0.0  \n",
       "TCGA-3C-AALK-01               0.0               0.0               0.0  \n",
       "TCGA-4H-AAAK-01               0.0               0.0               0.0  \n",
       "...                           ...               ...               ...  \n",
       "TCGA-WT-AB44-01               0.0               0.0               0.0  \n",
       "TCGA-XX-A899-01               0.0               0.0               0.0  \n",
       "TCGA-XX-A89A-01               0.0               0.0               0.0  \n",
       "TCGA-Z7-A8R5-01               0.0               0.0               0.0  \n",
       "TCGA-Z7-A8R6-01               0.0               0.0               0.0  \n",
       "\n",
       "[1098 rows x 14147 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data.get_results()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "62d482da-f15d-4b16-8df9-3559030997a7",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<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></th>\n",
       "      <th>(PARP1, BRCA2)</th>\n",
       "      <th>(AHR, CYP1B1)</th>\n",
       "      <th>(AHR, FOS)</th>\n",
       "      <th>(AHR, SOS1)</th>\n",
       "      <th>(AHR, UGT1A6)</th>\n",
       "      <th>(AR, ABCA1)</th>\n",
       "      <th>(AR, ABCA2)</th>\n",
       "      <th>(AR, ABCF1)</th>\n",
       "      <th>(AR, ABCA4)</th>\n",
       "      <th>(AR, ABL1)</th>\n",
       "      <th>...</th>\n",
       "      <th>(ZNF419, CDKN2A)</th>\n",
       "      <th>(ZNF671, CDKN2A)</th>\n",
       "      <th>(THAP7, CDKN2A)</th>\n",
       "      <th>(FOXP2, PLAUR)</th>\n",
       "      <th>(FOXP2, CNTNAP2)</th>\n",
       "      <th>(ZNF653, CDKN2A)</th>\n",
       "      <th>(E2F7, SP1)</th>\n",
       "      <th>(ZNF417, CDKN2A)</th>\n",
       "      <th>(ZNF384, CDKN2A)</th>\n",
       "      <th>(ZNF384, COL1A1)</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>patient id</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>TCGA-3C-AAAU-01</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TCGA-3C-AALI-01</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TCGA-3C-AALJ-01</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TCGA-3C-AALK-01</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TCGA-4H-AAAK-01</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</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",
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       "    <tr>\n",
       "      <th>TCGA-WT-AB44-01</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TCGA-XX-A899-01</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TCGA-XX-A89A-01</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TCGA-Z7-A8R5-01</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TCGA-Z7-A8R6-01</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1098 rows × 14147 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                 (PARP1, BRCA2)  (AHR, CYP1B1)  (AHR, FOS)  (AHR, SOS1)  \\\n",
       "patient id                                                                \n",
       "TCGA-3C-AAAU-01             0.0            0.0         0.0          0.0   \n",
       "TCGA-3C-AALI-01             0.0            0.0         0.0          0.0   \n",
       "TCGA-3C-AALJ-01             0.0            0.0         0.0          0.0   \n",
       "TCGA-3C-AALK-01             0.0            0.0         0.0          0.0   \n",
       "TCGA-4H-AAAK-01             0.0            0.0         0.0          0.0   \n",
       "...                         ...            ...         ...          ...   \n",
       "TCGA-WT-AB44-01             0.0            0.0         0.0          0.0   \n",
       "TCGA-XX-A899-01             0.0            0.0         0.0          0.0   \n",
       "TCGA-XX-A89A-01             0.0            0.0         0.0          0.0   \n",
       "TCGA-Z7-A8R5-01             0.0            0.0         0.0          0.0   \n",
       "TCGA-Z7-A8R6-01             0.0            0.0         0.0          0.0   \n",
       "\n",
       "                 (AHR, UGT1A6)  (AR, ABCA1)  (AR, ABCA2)  (AR, ABCF1)  \\\n",
       "patient id                                                              \n",
       "TCGA-3C-AAAU-01            0.0          0.0          0.0          0.0   \n",
       "TCGA-3C-AALI-01            0.0          0.0          0.0          0.0   \n",
       "TCGA-3C-AALJ-01            0.0          0.0          0.0          0.0   \n",
       "TCGA-3C-AALK-01            0.0          0.0          0.0          0.0   \n",
       "TCGA-4H-AAAK-01            0.0          0.0          0.0          0.0   \n",
       "...                        ...          ...          ...          ...   \n",
       "TCGA-WT-AB44-01            0.0          0.0          0.0          0.0   \n",
       "TCGA-XX-A899-01            0.0          0.0          0.0          0.0   \n",
       "TCGA-XX-A89A-01            0.0          0.0          0.0          0.0   \n",
       "TCGA-Z7-A8R5-01            0.0          0.0          0.0          0.0   \n",
       "TCGA-Z7-A8R6-01            0.0          0.0          0.0          0.0   \n",
       "\n",
       "                 (AR, ABCA4)  (AR, ABL1)  ...  (ZNF419, CDKN2A)  \\\n",
       "patient id                                ...                     \n",
       "TCGA-3C-AAAU-01          0.0         0.0  ...               0.0   \n",
       "TCGA-3C-AALI-01          0.0         0.0  ...               0.0   \n",
       "TCGA-3C-AALJ-01          0.0         0.0  ...               0.0   \n",
       "TCGA-3C-AALK-01          0.0         0.0  ...               0.0   \n",
       "TCGA-4H-AAAK-01          0.0         0.0  ...               0.0   \n",
       "...                      ...         ...  ...               ...   \n",
       "TCGA-WT-AB44-01          0.0         0.0  ...               0.0   \n",
       "TCGA-XX-A899-01          0.0         0.0  ...               0.0   \n",
       "TCGA-XX-A89A-01          0.0         0.0  ...               0.0   \n",
       "TCGA-Z7-A8R5-01          0.0         0.0  ...               0.0   \n",
       "TCGA-Z7-A8R6-01          0.0         0.0  ...               0.0   \n",
       "\n",
       "                 (ZNF671, CDKN2A)  (THAP7, CDKN2A)  (FOXP2, PLAUR)  \\\n",
       "patient id                                                           \n",
       "TCGA-3C-AAAU-01               0.0              0.0             0.0   \n",
       "TCGA-3C-AALI-01               0.0              0.0             0.0   \n",
       "TCGA-3C-AALJ-01               0.0              0.0             0.0   \n",
       "TCGA-3C-AALK-01               0.0              0.0             0.0   \n",
       "TCGA-4H-AAAK-01               0.0              0.0             0.0   \n",
       "...                           ...              ...             ...   \n",
       "TCGA-WT-AB44-01               0.0              0.0             0.0   \n",
       "TCGA-XX-A899-01               0.0              0.0             0.0   \n",
       "TCGA-XX-A89A-01               0.0              0.0             0.0   \n",
       "TCGA-Z7-A8R5-01               0.0              0.0             0.0   \n",
       "TCGA-Z7-A8R6-01               0.0              0.0             0.0   \n",
       "\n",
       "                 (FOXP2, CNTNAP2)  (ZNF653, CDKN2A)  (E2F7, SP1)  \\\n",
       "patient id                                                         \n",
       "TCGA-3C-AAAU-01               0.0               0.0          0.0   \n",
       "TCGA-3C-AALI-01               0.0               0.0          0.0   \n",
       "TCGA-3C-AALJ-01               0.0               0.0          0.0   \n",
       "TCGA-3C-AALK-01               0.0               0.0          0.0   \n",
       "TCGA-4H-AAAK-01               0.0               0.0          0.0   \n",
       "...                           ...               ...          ...   \n",
       "TCGA-WT-AB44-01               0.0               0.0          0.0   \n",
       "TCGA-XX-A899-01               0.0               0.0          0.0   \n",
       "TCGA-XX-A89A-01               0.0               0.0          0.0   \n",
       "TCGA-Z7-A8R5-01               0.0               0.0          0.0   \n",
       "TCGA-Z7-A8R6-01               0.0               0.0          0.0   \n",
       "\n",
       "                 (ZNF417, CDKN2A)  (ZNF384, CDKN2A)  (ZNF384, COL1A1)  \n",
       "patient id                                                             \n",
       "TCGA-3C-AAAU-01               0.0               0.0               0.0  \n",
       "TCGA-3C-AALI-01               0.0               0.0               0.0  \n",
       "TCGA-3C-AALJ-01               0.0               0.0               0.0  \n",
       "TCGA-3C-AALK-01               0.0               0.0               0.0  \n",
       "TCGA-4H-AAAK-01               0.0               0.0               0.0  \n",
       "...                           ...               ...               ...  \n",
       "TCGA-WT-AB44-01               0.0               0.0               0.0  \n",
       "TCGA-XX-A899-01               0.0               0.0               0.0  \n",
       "TCGA-XX-A89A-01               0.0               0.0               0.0  \n",
       "TCGA-Z7-A8R5-01               0.0               0.0               0.0  \n",
       "TCGA-Z7-A8R6-01               0.0               0.0               0.0  \n",
       "\n",
       "[1098 rows x 14147 columns]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data.get_results_binary()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "0aa5c03b-1886-4b06-a6dd-c7933a00046c",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th></th>\n",
       "      <th>R2</th>\n",
       "      <th>coef_intercept</th>\n",
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       "      <th>pval_race_BLACK OR AFRICAN AMERICAN</th>\n",
       "      <th>pval_race_WHITE</th>\n",
       "      <th>pval_race_[Not Evaluated]</th>\n",
       "      <th>pval_gender_MALE</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(PARP1, BRCA2)</th>\n",
       "      <td>0.518944</td>\n",
       "      <td>-0.628582</td>\n",
       "      <td>1.009024</td>\n",
       "      <td>0.000016</td>\n",
       "      <td>1.641409</td>\n",
       "      <td>1.672660</td>\n",
       "      <td>1.696522</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.119685</td>\n",
       "      <td>0.387606</td>\n",
       "      <td>2.496552e-14</td>\n",
       "      <td>0.196470</td>\n",
       "      <td>0.079281</td>\n",
       "      <td>0.019698</td>\n",
       "      <td>0.010310</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.852860</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(AHR, CYP1B1)</th>\n",
       "      <td>0.460382</td>\n",
       "      <td>-0.372820</td>\n",
       "      <td>0.524032</td>\n",
       "      <td>-0.000007</td>\n",
       "      <td>0.767510</td>\n",
       "      <td>0.131428</td>\n",
       "      <td>0.002362</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.155764</td>\n",
       "      <td>0.421093</td>\n",
       "      <td>2.162187e-14</td>\n",
       "      <td>0.355266</td>\n",
       "      <td>0.212239</td>\n",
       "      <td>0.782895</td>\n",
       "      <td>0.995718</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.716738</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(AHR, FOS)</th>\n",
       "      <td>0.075604</td>\n",
       "      <td>1.447006</td>\n",
       "      <td>0.005936</td>\n",
       "      <td>-0.000021</td>\n",
       "      <td>-1.688957</td>\n",
       "      <td>-0.004656</td>\n",
       "      <td>-0.260388</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.997901</td>\n",
       "      <td>0.077100</td>\n",
       "      <td>9.545845e-01</td>\n",
       "      <td>0.132889</td>\n",
       "      <td>0.118768</td>\n",
       "      <td>0.995564</td>\n",
       "      <td>0.736247</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.187290</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(AHR, SOS1)</th>\n",
       "      <td>0.469212</td>\n",
       "      <td>0.675038</td>\n",
       "      <td>0.764064</td>\n",
       "      <td>0.000008</td>\n",
       "      <td>-0.986869</td>\n",
       "      <td>-0.397666</td>\n",
       "      <td>-0.218486</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.340383</td>\n",
       "      <td>0.319415</td>\n",
       "      <td>2.434483e-14</td>\n",
       "      <td>0.491512</td>\n",
       "      <td>0.272152</td>\n",
       "      <td>0.568683</td>\n",
       "      <td>0.734236</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.034528</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(AHR, UGT1A6)</th>\n",
       "      <td>0.071785</td>\n",
       "      <td>-1.422249</td>\n",
       "      <td>0.133097</td>\n",
       "      <td>-0.000007</td>\n",
       "      <td>-0.751396</td>\n",
       "      <td>0.789607</td>\n",
       "      <td>1.100960</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.563332</td>\n",
       "      <td>0.147520</td>\n",
       "      <td>2.895810e-01</td>\n",
       "      <td>0.675375</td>\n",
       "      <td>0.561933</td>\n",
       "      <td>0.433673</td>\n",
       "      <td>0.237741</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.534613</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(ZNF653, CDKN2A)</th>\n",
       "      <td>0.261828</td>\n",
       "      <td>-2.962304</td>\n",
       "      <td>0.195867</td>\n",
       "      <td>-0.000037</td>\n",
       "      <td>0.956503</td>\n",
       "      <td>1.237842</td>\n",
       "      <td>1.233544</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-1.645633</td>\n",
       "      <td>0.000009</td>\n",
       "      <td>1.319707e-04</td>\n",
       "      <td>0.000767</td>\n",
       "      <td>0.250047</td>\n",
       "      <td>0.052591</td>\n",
       "      <td>0.038164</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.006131</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(E2F7, SP1)</th>\n",
       "      <td>0.231473</td>\n",
       "      <td>0.375956</td>\n",
       "      <td>0.302768</td>\n",
       "      <td>0.000028</td>\n",
       "      <td>0.878721</td>\n",
       "      <td>1.194801</td>\n",
       "      <td>1.148187</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.181981</td>\n",
       "      <td>0.576601</td>\n",
       "      <td>5.622973e-05</td>\n",
       "      <td>0.016079</td>\n",
       "      <td>0.318238</td>\n",
       "      <td>0.078094</td>\n",
       "      <td>0.070756</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.771183</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(ZNF417, CDKN2A)</th>\n",
       "      <td>0.183978</td>\n",
       "      <td>-2.813077</td>\n",
       "      <td>0.155436</td>\n",
       "      <td>-0.000037</td>\n",
       "      <td>0.672192</td>\n",
       "      <td>0.860186</td>\n",
       "      <td>0.882694</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-1.724703</td>\n",
       "      <td>0.000058</td>\n",
       "      <td>4.457482e-02</td>\n",
       "      <td>0.001722</td>\n",
       "      <td>0.451491</td>\n",
       "      <td>0.219116</td>\n",
       "      <td>0.170465</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.006266</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(ZNF384, CDKN2A)</th>\n",
       "      <td>0.165512</td>\n",
       "      <td>-3.017923</td>\n",
       "      <td>0.120197</td>\n",
       "      <td>-0.000036</td>\n",
       "      <td>0.915799</td>\n",
       "      <td>1.166994</td>\n",
       "      <td>1.129410</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-1.811391</td>\n",
       "      <td>0.000019</td>\n",
       "      <td>1.957493e-01</td>\n",
       "      <td>0.003156</td>\n",
       "      <td>0.303410</td>\n",
       "      <td>0.087805</td>\n",
       "      <td>0.075205</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.004527</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(ZNF384, COL1A1)</th>\n",
       "      <td>0.035308</td>\n",
       "      <td>-2.388996</td>\n",
       "      <td>0.016159</td>\n",
       "      <td>-0.000002</td>\n",
       "      <td>2.266961</td>\n",
       "      <td>1.227011</td>\n",
       "      <td>0.839028</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.528321</td>\n",
       "      <td>0.029983</td>\n",
       "      <td>9.138044e-01</td>\n",
       "      <td>0.914840</td>\n",
       "      <td>0.115510</td>\n",
       "      <td>0.263972</td>\n",
       "      <td>0.409823</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.601052</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>14147 rows × 17 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                        R2  coef_intercept   coef_TF  coef_birth_days_to  \\\n",
       "(PARP1, BRCA2)    0.518944       -0.628582  1.009024            0.000016   \n",
       "(AHR, CYP1B1)     0.460382       -0.372820  0.524032           -0.000007   \n",
       "(AHR, FOS)        0.075604        1.447006  0.005936           -0.000021   \n",
       "(AHR, SOS1)       0.469212        0.675038  0.764064            0.000008   \n",
       "(AHR, UGT1A6)     0.071785       -1.422249  0.133097           -0.000007   \n",
       "...                    ...             ...       ...                 ...   \n",
       "(ZNF653, CDKN2A)  0.261828       -2.962304  0.195867           -0.000037   \n",
       "(E2F7, SP1)       0.231473        0.375956  0.302768            0.000028   \n",
       "(ZNF417, CDKN2A)  0.183978       -2.813077  0.155436           -0.000037   \n",
       "(ZNF384, CDKN2A)  0.165512       -3.017923  0.120197           -0.000036   \n",
       "(ZNF384, COL1A1)  0.035308       -2.388996  0.016159           -0.000002   \n",
       "\n",
       "                  coef_race_ASIAN  coef_race_BLACK OR AFRICAN AMERICAN  \\\n",
       "(PARP1, BRCA2)           1.641409                             1.672660   \n",
       "(AHR, CYP1B1)            0.767510                             0.131428   \n",
       "(AHR, FOS)              -1.688957                            -0.004656   \n",
       "(AHR, SOS1)             -0.986869                            -0.397666   \n",
       "(AHR, UGT1A6)           -0.751396                             0.789607   \n",
       "...                           ...                                  ...   \n",
       "(ZNF653, CDKN2A)         0.956503                             1.237842   \n",
       "(E2F7, SP1)              0.878721                             1.194801   \n",
       "(ZNF417, CDKN2A)         0.672192                             0.860186   \n",
       "(ZNF384, CDKN2A)         0.915799                             1.166994   \n",
       "(ZNF384, COL1A1)         2.266961                             1.227011   \n",
       "\n",
       "                  coef_race_WHITE  coef_race_[Not Evaluated]  \\\n",
       "(PARP1, BRCA2)           1.696522                        0.0   \n",
       "(AHR, CYP1B1)            0.002362                        0.0   \n",
       "(AHR, FOS)              -0.260388                        0.0   \n",
       "(AHR, SOS1)             -0.218486                        0.0   \n",
       "(AHR, UGT1A6)            1.100960                        0.0   \n",
       "...                           ...                        ...   \n",
       "(ZNF653, CDKN2A)         1.233544                        0.0   \n",
       "(E2F7, SP1)              1.148187                        0.0   \n",
       "(ZNF417, CDKN2A)         0.882694                        0.0   \n",
       "(ZNF384, CDKN2A)         1.129410                        0.0   \n",
       "(ZNF384, COL1A1)         0.839028                        0.0   \n",
       "\n",
       "                  coef_gender_MALE  pval_intercept       pval_TF  \\\n",
       "(PARP1, BRCA2)           -0.119685        0.387606  2.496552e-14   \n",
       "(AHR, CYP1B1)            -0.155764        0.421093  2.162187e-14   \n",
       "(AHR, FOS)                0.997901        0.077100  9.545845e-01   \n",
       "(AHR, SOS1)               1.340383        0.319415  2.434483e-14   \n",
       "(AHR, UGT1A6)             0.563332        0.147520  2.895810e-01   \n",
       "...                            ...             ...           ...   \n",
       "(ZNF653, CDKN2A)         -1.645633        0.000009  1.319707e-04   \n",
       "(E2F7, SP1)               0.181981        0.576601  5.622973e-05   \n",
       "(ZNF417, CDKN2A)         -1.724703        0.000058  4.457482e-02   \n",
       "(ZNF384, CDKN2A)         -1.811391        0.000019  1.957493e-01   \n",
       "(ZNF384, COL1A1)          0.528321        0.029983  9.138044e-01   \n",
       "\n",
       "                  pval_birth_days_to  pval_race_ASIAN  \\\n",
       "(PARP1, BRCA2)              0.196470         0.079281   \n",
       "(AHR, CYP1B1)               0.355266         0.212239   \n",
       "(AHR, FOS)                  0.132889         0.118768   \n",
       "(AHR, SOS1)                 0.491512         0.272152   \n",
       "(AHR, UGT1A6)               0.675375         0.561933   \n",
       "...                              ...              ...   \n",
       "(ZNF653, CDKN2A)            0.000767         0.250047   \n",
       "(E2F7, SP1)                 0.016079         0.318238   \n",
       "(ZNF417, CDKN2A)            0.001722         0.451491   \n",
       "(ZNF384, CDKN2A)            0.003156         0.303410   \n",
       "(ZNF384, COL1A1)            0.914840         0.115510   \n",
       "\n",
       "                  pval_race_BLACK OR AFRICAN AMERICAN  pval_race_WHITE  \\\n",
       "(PARP1, BRCA2)                               0.019698         0.010310   \n",
       "(AHR, CYP1B1)                                0.782895         0.995718   \n",
       "(AHR, FOS)                                   0.995564         0.736247   \n",
       "(AHR, SOS1)                                  0.568683         0.734236   \n",
       "(AHR, UGT1A6)                                0.433673         0.237741   \n",
       "...                                               ...              ...   \n",
       "(ZNF653, CDKN2A)                             0.052591         0.038164   \n",
       "(E2F7, SP1)                                  0.078094         0.070756   \n",
       "(ZNF417, CDKN2A)                             0.219116         0.170465   \n",
       "(ZNF384, CDKN2A)                             0.087805         0.075205   \n",
       "(ZNF384, COL1A1)                             0.263972         0.409823   \n",
       "\n",
       "                  pval_race_[Not Evaluated]  pval_gender_MALE  \n",
       "(PARP1, BRCA2)                          NaN          0.852860  \n",
       "(AHR, CYP1B1)                           NaN          0.716738  \n",
       "(AHR, FOS)                              NaN          0.187290  \n",
       "(AHR, SOS1)                             NaN          0.034528  \n",
       "(AHR, UGT1A6)                           NaN          0.534613  \n",
       "...                                     ...               ...  \n",
       "(ZNF653, CDKN2A)                        NaN          0.006131  \n",
       "(E2F7, SP1)                             NaN          0.771183  \n",
       "(ZNF417, CDKN2A)                        NaN          0.006266  \n",
       "(ZNF384, CDKN2A)                        NaN          0.004527  \n",
       "(ZNF384, COL1A1)                        NaN          0.601052  \n",
       "\n",
       "[14147 rows x 17 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data.get_model_stats()"
   ]
  }
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