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        "description": "What is logloss-beraf?\n----------------------\n\nA tool for selection of a limited number of informative DNA methylation\nregions (i.e. sites) based on a combination of several feature selection\nmethods and an ensemble-based classifier. It is expected to handle higly\nunbalanced and heterogeneous data. Also it is intended for the design\nof diagnostic panels that can be potentially used in routine laboratory practice.\n\nQuick start\n-----------\n\n1. Install ``logloss-beraf`` with all the dependencies::\n\n        easy_install logloss-beraf\n\n2. Make a test run. It uses data included to the package::\n\n        logloss_beraf test_run\n\n3. Prepare input feature and annotation tables (in CSV format). The order of samples in those tables is supposed to be the same\n\n```\n     # Methylation data\n                Feature_1 Feature_2  Feature_3\n     Sample_0   0.909642  0.823715   0.069785\n     Sample_1   0.564799  0.199724   0.840741\n     Sample_2   0.685081  0.489773   0.286591\n     Sample_3   0.810637  0.006836   0.888038\n     Sample_4   0.124098  0.347752   0.954853\n```\n\n\n```\n     # Annotation data\n     Sample_Name  Type\n     Sample_0     Benign\n     Sample_1     Pathologic\n     Sample_2     Benign\n     Sample_3     Benign\n     Sample_4     Pathologic\n ```\n\n4. `Train model`\n\n```sh\nlogloss_beraf train \\\n    --features path_to_feature_table \\\n    --features_max_num 10 \\\n    --min_beta_threshold 0.2 \\\n    --annotation path_to_annotation_table \\\n    --sample_name_column \"Sample_Name\" \\\n    --class_column \"Type\" \\\n    --output_folder path_to_output_folder\n```\n\n5. `Apply trained model to independent dataset`\n\n```sh\nlogloss_beraf apply \\\n  --features path_to_test_feature_table \\\n  --model path_to_trained_model\n  --output_folder path_to_output_folder\n ```\n\n\n\n\n",
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