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"source": [
"# Quickstart\n",
"\n",
"Train and run MethylSeg on a WGBS or TCGA HM450K sample."
]
},
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"cell_type": "code",
"execution_count": 4,
"id": "7ce01fb5",
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"name": "stdout",
"output_type": "stream",
"text": [
"Fitting pathway...\n",
"Generating regions ...\n"
]
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" \n",
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""
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"source": [
"from pathlib import Path\n",
"\n",
"from methylseg import MethylSegPathway, MethylationStates\n",
"from methylseg.helper_classes import DATA_DIR\n",
"\n",
"reference_dir = DATA_DIR / \"reference_files\"\n",
"\n",
"# WGBS: replace these with your own sample name and count table.\n",
"# sample_name = \"WGBS_colon-primary-tumor_1\"\n",
"# sample_file = reference_dir / \"WGBS_colon-primary-tumor_1_wgbs.tsv.gz\"\n",
"# resolution = \"wgbs\"\n",
"\n",
"# TCGA/HM450K alternative:\n",
"sample_name = \"TCGA-BD-A3EP-01A\"\n",
"sample_file = reference_dir / \"TCGA-BD-A3EP-01A_450k.tsv.gz\"\n",
"resolution = \"450k\"\n",
"\n",
"sample_info, removed_df = MethylSegPathway.prepare_sample_info(\n",
" sample_name=sample_name,\n",
" sample_file=sample_file,\n",
" resolution=resolution,\n",
" remove_low_coverage_like_cpgs=True,\n",
")\n",
"\n",
"pathway = MethylSegPathway(\n",
" train_sample_info=sample_info,\n",
" out_dir=Path(\"out/quickstart\") / sample_name,\n",
")\n",
"\n",
"pathway.run_pathway()\n",
"\n",
"fig = pathway.plot_labels(\n",
" sample_info=sample_info,\n",
" sample_info_removed=removed_df,\n",
" chrom=\"chr1\",\n",
" region_start=2_200_000,\n",
" region_end=3_700_000\n",
")\n"
]
}
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