{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Part 2 - Patient Similarity Networks (PSNs)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Table of Contents" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Part 2.\n", "\n", "10. **Patient Similarity Network Construction**\n", "\n", "11. **DNA Methylation Network Analysis** " ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "# standard libraries\n", "import os\n", "import pickle\n", "\n", "# scientific and data manipulation libraries\n", "import numpy as np\n", "import pandas as pd\n", "from scipy import stats\n", "from sklearn.feature_selection import mutual_info_regression\n", "from astropy.stats import median_absolute_deviation\n", "import mygene\n", "import astropy\n", "\n", "# graph and network libraries\n", "import networkx as nx\n", "\n", "# visualization libraries\n", "import matplotlib.pyplot as plt\n", "import seaborn as sns\n", "import plotly.graph_objects as go\n", "import plotly.io as pio\n", "from IPython.display import Image\n", "from IPython.display import display\n", "\n", "import warnings\n", "warnings.filterwarnings('ignore')\n", "\n", "# import custom functions from the previous notebook\n", "import sys\n", "sys.path.insert(0 , '/tutorial/')\n", "from functions import *" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# 10. Patient Similarity Network (PSN)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "- Based on the same expression matrix we can create a patient similarity network.\n", "- Transposing the matrix will switch the rows and columns,\n", "- meaning that patients will become the columns instead of genes\n", "- By doing this, you can compute the correlation (or similarity) between patients based on their gene expression profiles,\n", "- and then create a network where nodes represent patients and edges represent similarities." ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [], "source": [ "# main data directories for the project\n", "\n", "raw_data_dir = '/data/raw'\n", "intermediate_data_dir = '/data/intermediate'" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [], "source": [ "# read in os.path.join(intermediate_data_dir,\"expression_data_filtered.csv\")\n", "df_renamed = pd.read_csv(os.path.join(intermediate_data_dir,\n", " \"expression_data_filtered.csv\"),\n", " index_col=0)" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [], "source": [ "'''\n", "#################################################\n", " YOUR CODE HERE\n", "#################################################\n", "\n", "We will now transpose the df_renamed df so that the rows represent the genes and the columns represent the patients.\n", "Let's call the transposed df patient_gene_matrix.\n", "\n", "'''\n", "\n", "patient_gene_matrix = df_renamed.T" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
A2M | \n", "17.7492 | \n", "14.8513 | \n", "14.1691 | \n", "16.7238 | \n", "15.6783 | \n", "14.7566 | \n", "16.4368 | \n", "15.5476 | \n", "15.5478 | \n", "15.1337 | \n", "... | \n", "15.9553 | \n", "13.9511 | \n", "16.3097 | \n", "14.3934 | \n", "15.8254 | \n", "16.3773 | \n", "14.9411 | \n", "16.7343 | \n", "15.6622 | \n", "14.8136 | \n", "
A2ML1 | \n", "4.4411 | \n", "4.4530 | \n", "4.5026 | \n", "3.1704 | \n", "4.7422 | \n", "6.0918 | \n", "4.0602 | \n", "3.0827 | \n", "3.4608 | \n", "3.6367 | \n", "... | \n", "4.7076 | \n", "2.4821 | \n", "8.0810 | \n", "3.3415 | \n", "5.3379 | \n", "4.0817 | \n", "6.7210 | \n", "5.2575 | \n", "3.7345 | \n", "4.3058 | \n", "
A4GALT | \n", "10.1862 | \n", "8.9312 | \n", "9.0834 | \n", "9.1443 | \n", "9.5150 | \n", "11.4452 | \n", "9.1462 | \n", "7.3597 | \n", "9.1602 | \n", "8.9344 | \n", "... | \n", "9.1019 | \n", "8.6653 | \n", "10.8837 | \n", "8.6304 | \n", "9.3827 | \n", "9.4234 | \n", "11.9107 | \n", "9.5379 | \n", "9.8660 | \n", "9.7702 | \n", "
AACSP1 | \n", "3.5845 | \n", "3.6762 | \n", "3.8623 | \n", "2.4821 | \n", "3.2271 | \n", "2.4821 | \n", "5.6614 | \n", "3.0827 | \n", "3.9428 | \n", "4.7089 | \n", "... | \n", "5.4947 | \n", "3.0956 | \n", "2.4821 | \n", "3.7710 | \n", "2.9397 | \n", "6.6519 | \n", "8.8283 | \n", "2.4821 | \n", "4.1045 | \n", "6.8425 | \n", "
AADAC | \n", "9.6415 | \n", "6.5685 | \n", "5.5634 | \n", "4.3206 | \n", "7.2321 | \n", "6.8821 | \n", "8.1176 | \n", "4.7935 | \n", "11.7750 | \n", "7.0644 | \n", "... | \n", "9.0856 | \n", "3.8162 | \n", "5.6471 | \n", "4.6785 | \n", "4.6578 | \n", "6.7641 | \n", "3.4947 | \n", "5.7120 | \n", "6.2214 | \n", "5.2016 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
ZSCAN23 | \n", "5.7385 | \n", "4.3796 | \n", "5.6728 | \n", "3.6533 | \n", "5.0478 | \n", "6.0489 | \n", "5.8058 | \n", "3.7897 | \n", "4.3451 | \n", "5.5259 | \n", "... | \n", "4.7076 | \n", "2.4821 | \n", "4.6683 | \n", "3.4697 | \n", "4.3516 | \n", "7.2074 | \n", "6.9167 | \n", "6.0927 | \n", "5.3854 | \n", "3.6792 | \n", "
ZSCAN31 | \n", "9.0817 | \n", "10.9565 | \n", "10.8095 | \n", "8.9874 | \n", "9.5810 | \n", "9.0185 | \n", "10.2085 | \n", "9.8803 | \n", "11.0327 | \n", "10.2707 | \n", "... | \n", "9.2033 | \n", "10.5020 | \n", "8.8073 | \n", "9.8672 | \n", "10.6419 | \n", "10.2410 | \n", "9.4672 | \n", "10.0507 | \n", "7.4843 | \n", "8.5268 | \n", "
ZSCAN4 | \n", "3.2709 | \n", "3.0918 | \n", "2.4821 | \n", "3.4468 | \n", "3.0118 | \n", "5.0894 | \n", "5.5341 | \n", "3.5082 | \n", "5.4987 | \n", "3.3645 | \n", "... | \n", "4.4088 | \n", "7.4937 | \n", "4.3167 | \n", "5.0907 | \n", "6.7676 | \n", "5.1126 | \n", "3.3143 | \n", "4.2816 | \n", "4.4650 | \n", "2.4821 | \n", "
ZWINT | \n", "9.2615 | \n", "10.1334 | \n", "10.9149 | \n", "9.7828 | \n", "8.6640 | \n", "11.1212 | \n", "9.0718 | \n", "10.7305 | \n", "9.0013 | \n", "10.4268 | \n", "... | \n", "9.7614 | \n", "10.7593 | \n", "9.7087 | \n", "10.4729 | \n", "10.9794 | \n", "10.1390 | \n", "10.0583 | \n", "9.4627 | \n", "9.5817 | \n", "10.8228 | \n", "
ZYG11A | \n", "4.0073 | \n", "8.3219 | \n", "6.7593 | \n", "3.4468 | \n", "4.7844 | \n", "5.0894 | \n", "9.4014 | \n", "4.7935 | \n", "4.2748 | \n", "7.1709 | \n", "... | \n", "6.5412 | \n", "7.1933 | \n", "5.8778 | \n", "7.3822 | \n", "8.7596 | \n", "8.2478 | \n", "8.4566 | \n", "7.4014 | \n", "4.6804 | \n", "8.6068 | \n", "
5338 rows × 498 columns
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
TCGA-55-7914 | \n", "0.039144 | \n", "0.078881 | \n", "0.032201 | \n", "0.098520 | \n", "0.971626 | \n", "0.020020 | \n", "0.929670 | \n", "0.033325 | \n", "0.043767 | \n", "0.028051 | \n", "... | \n", "0.053027 | \n", "0.046047 | \n", "0.951328 | \n", "0.045767 | \n", "0.048185 | \n", "0.014262 | \n", "0.034541 | \n", "0.034967 | \n", "0.041538 | \n", "0.053116 | \n", "
TCGA-38-4631 | \n", "0.954805 | \n", "0.047287 | \n", "0.027976 | \n", "0.925794 | \n", "0.144636 | \n", "0.365842 | \n", "0.156414 | \n", "0.027917 | \n", "0.047609 | \n", "0.049901 | \n", "... | \n", "0.048398 | \n", "0.047221 | \n", "0.939891 | \n", "0.056141 | \n", "0.047459 | \n", "0.014548 | \n", "0.056591 | \n", "0.039086 | \n", "0.044946 | \n", "0.055473 | \n", "
TCGA-73-4658 | \n", "0.966071 | \n", "0.126549 | \n", "0.030316 | \n", "0.945166 | \n", "0.976080 | \n", "0.975638 | \n", "0.942018 | \n", "0.066659 | \n", "0.052100 | \n", "0.047054 | \n", "... | \n", "0.040815 | \n", "0.042040 | \n", "0.951235 | \n", "0.045477 | \n", "0.074037 | \n", "0.019053 | \n", "0.029978 | \n", "0.039345 | \n", "0.060650 | \n", "0.041385 | \n", "
TCGA-50-5932 | \n", "0.965140 | \n", "0.061194 | \n", "0.935457 | \n", "0.923421 | \n", "0.965443 | \n", "0.027598 | \n", "0.040885 | \n", "0.036178 | \n", "0.045745 | \n", "0.046439 | \n", "... | \n", "0.057840 | \n", "0.045106 | \n", "0.948255 | \n", "0.044558 | \n", "0.039484 | \n", "0.013837 | \n", "0.037048 | \n", "0.032503 | \n", "0.058576 | \n", "0.037666 | \n", "
TCGA-55-7576 | \n", "0.958612 | \n", "0.071607 | \n", "0.027077 | \n", "0.940574 | \n", "0.976870 | \n", "0.785073 | \n", "0.953674 | \n", "0.945107 | \n", "0.056088 | \n", "0.955472 | \n", "... | \n", "0.046921 | \n", "0.051442 | \n", "0.954000 | \n", "0.034352 | \n", "0.031497 | \n", "0.014924 | \n", "0.035520 | \n", "0.043547 | \n", "0.056388 | \n", "0.052208 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
TCGA-50-8457 | \n", "0.960316 | \n", "0.940219 | \n", "0.046927 | \n", "0.942980 | \n", "0.977751 | \n", "0.633731 | \n", "0.940723 | \n", "0.053398 | \n", "0.059292 | \n", "0.968875 | \n", "... | \n", "0.047640 | \n", "0.062680 | \n", "0.954824 | \n", "0.043137 | \n", "0.048599 | \n", "0.014066 | \n", "0.031109 | \n", "0.039247 | \n", "0.035110 | \n", "0.054273 | \n", "
TCGA-91-6840 | \n", "0.964250 | \n", "0.921250 | \n", "0.957943 | \n", "0.958416 | \n", "0.981439 | \n", "0.278432 | \n", "0.968525 | \n", "0.032143 | \n", "0.083996 | \n", "0.037912 | \n", "... | \n", "0.045197 | \n", "0.066271 | \n", "0.963420 | \n", "0.047621 | \n", "0.060854 | \n", "0.015823 | \n", "0.045674 | \n", "0.040006 | \n", "0.052008 | \n", "0.040826 | \n", "
TCGA-86-8280 | \n", "0.948855 | \n", "0.942925 | \n", "0.958506 | \n", "0.945667 | \n", "0.970511 | \n", "0.544447 | \n", "0.921924 | \n", "0.939427 | \n", "0.082121 | \n", "0.045036 | \n", "... | \n", "0.062367 | \n", "0.058898 | \n", "0.954355 | \n", "0.045702 | \n", "0.048930 | \n", "0.019321 | \n", "0.039341 | \n", "0.036627 | \n", "0.054269 | \n", "0.056795 | \n", "
TCGA-95-A4VK | \n", "0.037255 | \n", "0.050940 | \n", "0.036565 | \n", "0.098237 | \n", "0.976780 | \n", "0.683394 | \n", "0.960073 | \n", "0.025232 | \n", "0.062487 | \n", "0.026908 | \n", "... | \n", "0.056248 | \n", "0.053591 | \n", "0.947020 | \n", "0.035344 | \n", "0.057783 | \n", "0.010943 | \n", "0.051868 | \n", "0.035566 | \n", "0.044910 | \n", "0.042269 | \n", "
TCGA-55-6969 | \n", "0.945954 | \n", "0.068404 | \n", "0.923325 | \n", "0.930684 | \n", "0.962295 | \n", "0.037952 | \n", "0.153943 | \n", "0.033980 | \n", "0.056811 | \n", "0.050211 | \n", "... | \n", "0.048765 | \n", "0.061228 | \n", "0.930596 | \n", "0.056050 | \n", "0.061802 | \n", "0.017861 | \n", "0.044229 | \n", "0.054682 | \n", "0.045090 | \n", "0.064186 | \n", "
459 rows × 300000 columns
\n", "\n", " | author | \n", "consortium | \n", "pmid | \n", "date | \n", "trait | \n", "efo | \n", "analysis | \n", "source | \n", "outcome | \n", "exposure | \n", "... | \n", "chrpos | \n", "chr | \n", "pos | \n", "gene | \n", "type | \n", "beta | \n", "se | \n", "p | \n", "details | \n", "study_id | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "Sikdar S | \n", "CHARGE | \n", "31536415 | \n", "2019-09-19 | \n", "Smoking | \n", "EFO_0009115, EFO_0006527, EFO_0004318 | \n", "random effects meta-analysis | \n", "Table S2 | \n", "DNA methylation | \n", "Smoking | \n", "... | \n", "chr2:233284934 | \n", "2 | \n", "233284934 | \n", "- | \n", "Island | \n", "-0.08545 | \n", "0.00131 | \n", "0.000000 | \n", "NaN | \n", "31536415_Sikdar-S_smoking_random_effects_meta-... | \n", "
1 | \n", "Sikdar S | \n", "CHARGE | \n", "31536415 | \n", "2019-09-19 | \n", "Smoking | \n", "EFO_0009115, EFO_0006527, EFO_0004318 | \n", "random effects meta-analysis | \n", "Table S2 | \n", "DNA methylation | \n", "Smoking | \n", "... | \n", "chr19:17000585 | \n", "19 | \n", "17000585 | \n", "F2RL3 | \n", "North shore | \n", "-0.07233 | \n", "0.00129 | \n", "0.000000 | \n", "NaN | \n", "31536415_Sikdar-S_smoking_random_effects_meta-... | \n", "
2 | \n", "Sikdar S | \n", "CHARGE | \n", "31536415 | \n", "2019-09-19 | \n", "Smoking | \n", "EFO_0009115, EFO_0006527, EFO_0004318 | \n", "random effects meta-analysis | \n", "Table S2 | \n", "DNA methylation | \n", "Smoking | \n", "... | \n", "chr5:373378 | \n", "5 | \n", "373378 | \n", "AHRR | \n", "North shore | \n", "-0.03138 | \n", "0.00078 | \n", "0.000000 | \n", "NaN | \n", "31536415_Sikdar-S_smoking_random_effects_meta-... | \n", "
3 | \n", "Sikdar S | \n", "CHARGE | \n", "31536415 | \n", "2019-09-19 | \n", "Smoking | \n", "EFO_0009115, EFO_0006527, EFO_0004318 | \n", "random effects meta-analysis | \n", "Table S2 | \n", "DNA methylation | \n", "Smoking | \n", "... | \n", "chr2:233284402 | \n", "2 | \n", "233284402 | \n", "- | \n", "Island | \n", "-0.07381 | \n", "0.00132 | \n", "0.000000 | \n", "NaN | \n", "31536415_Sikdar-S_smoking_random_effects_meta-... | \n", "
4 | \n", "Sikdar S | \n", "CHARGE | \n", "31536415 | \n", "2019-09-19 | \n", "Smoking | \n", "EFO_0009115, EFO_0006527, EFO_0004318 | \n", "random effects meta-analysis | \n", "Table S2 | \n", "DNA methylation | \n", "Smoking | \n", "... | \n", "chr6:30720080 | \n", "6 | \n", "30720080 | \n", "- | \n", "Open sea | \n", "-0.08558 | \n", "0.00159 | \n", "0.000000 | \n", "NaN | \n", "31536415_Sikdar-S_smoking_random_effects_meta-... | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
40124 | \n", "Domingo-Relloso A | \n", "Strong Heart Study | \n", "32484362 | \n", "2020-06-02 | \n", "Smoking | \n", "EFO_0004318, EFO_0005671, EFO_0006527 | \n", "Former vs never | \n", "Table S3 | \n", "DNA methylation | \n", "Smoking | \n", "... | \n", "chr6:32118295 | \n", "6 | \n", "32118295 | \n", "PRRT1 | \n", "Island | \n", "-0.05100 | \n", "0.01310 | \n", "0.000099 | \n", "NaN | \n", "32484362_Domingo-Relloso-A_smoking_former_vs_n... | \n", "
40125 | \n", "Domingo-Relloso A | \n", "Strong Heart Study | \n", "32484362 | \n", "2020-06-02 | \n", "Smoking | \n", "EFO_0004318, EFO_0005671, EFO_0006527 | \n", "Former vs never | \n", "Table S3 | \n", "DNA methylation | \n", "Smoking | \n", "... | \n", "chr1:75599645 | \n", "1 | \n", "75599645 | \n", "LHX8 | \n", "North shore | \n", "-0.07300 | \n", "0.01880 | \n", "0.000099 | \n", "NaN | \n", "32484362_Domingo-Relloso-A_smoking_former_vs_n... | \n", "
40126 | \n", "Domingo-Relloso A | \n", "Strong Heart Study | \n", "32484362 | \n", "2020-06-02 | \n", "Smoking | \n", "EFO_0004318, EFO_0005671, EFO_0006526 | \n", "Pack years | \n", "Table S4 | \n", "DNA methylation | \n", "Smoking | \n", "... | \n", "chr6:25992047 | \n", "6 | \n", "25992047 | \n", "- | \n", "North shore | \n", "0.00268 | \n", "0.00070 | \n", "0.000099 | \n", "NaN | \n", "32484362_Domingo-Relloso-A_smoking_pack_years | \n", "
40127 | \n", "Domingo-Relloso A | \n", "Strong Heart Study | \n", "32484362 | \n", "2020-06-02 | \n", "Smoking | \n", "EFO_0004318, EFO_0005671, EFO_0006526 | \n", "Pack years | \n", "Table S4 | \n", "DNA methylation | \n", "Smoking | \n", "... | \n", "chr10:33421027 | \n", "10 | \n", "33421027 | \n", "- | \n", "Open sea | \n", "0.00112 | \n", "0.00030 | \n", "0.000099 | \n", "NaN | \n", "32484362_Domingo-Relloso-A_smoking_pack_years | \n", "
40128 | \n", "Domingo-Relloso A | \n", "Strong Heart Study | \n", "32484362 | \n", "2020-06-02 | \n", "Smoking | \n", "EFO_0004318, EFO_0005671, EFO_0006526 | \n", "Pack years | \n", "Table S4 | \n", "DNA methylation | \n", "Smoking | \n", "... | \n", "chr15:41895799 | \n", "15 | \n", "41895799 | \n", "- | \n", "Open sea | \n", "0.00109 | \n", "0.00030 | \n", "0.000099 | \n", "NaN | \n", "32484362_Domingo-Relloso-A_smoking_pack_years | \n", "
40129 rows × 31 columns
\n", "\n", " | TCGA-75-6205 | \n", "TCGA-97-7941 | \n", "TCGA-97-7547 | \n", "TCGA-95-7567 | \n", "TCGA-95-7944 | \n", "TCGA-69-7979 | \n", "TCGA-55-7913 | \n", "TCGA-55-8206 | \n", "TCGA-55-6986 | \n", "TCGA-64-5779 | \n", "... | \n", "TCGA-91-8497 | \n", "TCGA-MP-A4TC | \n", "TCGA-J2-8194 | \n", "TCGA-75-7030 | \n", "TCGA-50-5942 | \n", "TCGA-86-7954 | \n", "TCGA-78-7145 | \n", "TCGA-62-A46R | \n", "TCGA-L9-A7SV | \n", "TCGA-86-8279 | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
cg01731783 | \n", "0.497444 | \n", "0.396698 | \n", "0.396081 | \n", "0.403062 | \n", "0.498713 | \n", "0.411565 | \n", "0.524197 | \n", "0.400507 | \n", "0.417326 | \n", "0.518443 | \n", "... | \n", "0.446258 | \n", "0.568588 | \n", "0.437242 | \n", "0.452883 | \n", "0.327272 | \n", "0.467690 | \n", "0.311361 | \n", "0.421168 | \n", "0.481429 | \n", "0.429422 | \n", "
cg25949550 | \n", "0.317716 | \n", "0.140767 | \n", "0.200784 | \n", "0.483062 | \n", "0.149553 | \n", "0.259965 | \n", "0.110951 | \n", "0.144628 | \n", "0.415628 | \n", "0.165865 | \n", "... | \n", "0.200756 | \n", "0.206802 | \n", "0.227245 | \n", "0.205266 | \n", "0.231608 | \n", "0.159593 | \n", "0.193704 | \n", "0.331710 | \n", "0.147767 | \n", "0.137870 | \n", "
cg18316974 | \n", "0.843950 | \n", "0.579421 | \n", "0.750254 | \n", "0.879412 | \n", "0.626643 | \n", "0.192301 | \n", "0.651054 | \n", "0.810144 | \n", "0.696567 | \n", "0.545015 | \n", "... | \n", "0.497423 | \n", "0.680952 | \n", "0.433783 | \n", "0.515681 | \n", "0.626869 | \n", "0.515729 | \n", "0.903988 | \n", "0.860906 | \n", "0.725199 | \n", "0.371918 | \n", "
cg17372101 | \n", "0.391085 | \n", "0.602731 | \n", "0.729051 | \n", "0.349166 | \n", "0.423132 | \n", "0.378651 | \n", "0.326185 | \n", "0.575440 | \n", "0.607495 | \n", "0.251461 | \n", "... | \n", "0.571380 | \n", "0.254356 | \n", "0.269948 | \n", "0.499414 | \n", "0.516246 | \n", "0.357175 | \n", "0.171478 | \n", "0.269681 | \n", "0.134351 | \n", "0.192490 | \n", "
cg18146737 | \n", "0.650549 | \n", "0.442971 | \n", "0.438343 | \n", "0.735122 | \n", "0.543430 | \n", "0.184128 | \n", "0.498125 | \n", "0.386880 | \n", "0.554262 | \n", "0.494514 | \n", "... | \n", "0.407518 | \n", "0.578550 | \n", "0.345746 | \n", "0.446022 | \n", "0.401742 | \n", "0.427868 | \n", "0.415197 | \n", "0.753086 | \n", "0.364550 | \n", "0.419654 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
cg12803068 | \n", "0.820755 | \n", "0.664510 | \n", "0.890526 | \n", "0.899519 | \n", "0.858862 | \n", "0.817286 | \n", "0.699223 | \n", "0.796747 | \n", "0.589624 | \n", "0.692833 | \n", "... | \n", "0.690219 | \n", "0.766702 | \n", "0.676125 | \n", "0.582260 | \n", "0.755870 | \n", "0.683585 | \n", "0.901678 | \n", "0.796409 | \n", "0.748843 | \n", "0.822947 | \n", "
cg01207684 | \n", "0.508975 | \n", "0.187581 | \n", "0.124399 | \n", "0.299321 | \n", "0.538336 | \n", "0.128008 | \n", "0.331944 | \n", "0.184965 | \n", "0.290967 | \n", "0.246457 | \n", "... | \n", "0.251051 | \n", "0.352854 | \n", "0.128596 | \n", "0.280396 | \n", "0.163345 | \n", "0.287115 | \n", "0.113246 | \n", "0.338427 | \n", "0.101977 | \n", "0.099196 | \n", "
cg25305703 | \n", "0.750465 | \n", "0.858270 | \n", "0.358668 | \n", "0.315991 | \n", "0.804947 | \n", "0.682358 | \n", "0.732886 | \n", "0.861646 | \n", "0.820864 | \n", "0.488925 | \n", "... | \n", "0.861702 | \n", "0.685447 | \n", "0.810510 | \n", "0.811707 | \n", "0.907132 | \n", "0.818094 | \n", "0.597665 | \n", "0.818712 | \n", "0.111031 | \n", "0.356221 | \n", "
cg14580211 | \n", "0.852855 | \n", "0.760703 | \n", "0.877694 | \n", "0.837730 | \n", "0.819975 | \n", "0.874536 | \n", "0.639945 | \n", "0.844139 | \n", "0.851723 | \n", "0.789981 | \n", "... | \n", "0.845984 | \n", "0.648610 | \n", "0.715354 | \n", "0.746873 | \n", "0.822599 | \n", "0.887925 | \n", "0.913990 | \n", "0.834070 | \n", "0.940591 | \n", "0.797121 | \n", "
cg18446336 | \n", "0.659491 | \n", "0.637922 | \n", "0.815690 | \n", "0.795733 | \n", "0.763106 | \n", "0.813799 | \n", "0.723343 | \n", "0.828749 | \n", "0.682581 | \n", "0.751079 | \n", "... | \n", "0.749783 | \n", "0.687554 | \n", "0.643351 | \n", "0.789296 | \n", "0.756348 | \n", "0.712804 | \n", "0.820558 | \n", "0.760244 | \n", "0.842471 | \n", "0.862028 | \n", "
112 rows × 442 columns
\n", "