Metadata-Version: 1.1
Name: logloss-beraf
Version: 0.1
Summary: A tool for costructing a limited sized diagnostic panels based on methylation data
Home-page: UNKNOWN
Author: dezzan
Author-email: dezzandev@gmail.com
License: GPLv3
Description: What is logloss-beraf?
        ----------------------
        
        A tool for selection of a limited number of informative DNA methylation
        regions (i.e. sites) based on a combination of several feature selection
        methods and an ensemble-based classifier. It is expected to handle higly
        unbalanced and heterogeneous data. Also it is intended for the design
        of diagnostic panels that can be potentially used in routine laboratory practice.
        
        Quick start
        -----------
        
        1. `Install`_ ``logloss-beraf`` with all the dependencies::
            ```bash
            pip install logloss_beraf
            ```
        
        2. `Make a test run`. It uses test data included to the package
            ```bash
            logloss_beraf test_run
            ```
        
        3. `Prepare input feature and annotation tables.` The order of samples in those tables is supposed to be the same
            Methylation data
            ```
                       Feature_1 Feature_2  Feature_3
            Sample_0   0.909642  0.823715   0.069785
            Sample_1   0.564799  0.199724   0.840741
            Sample_2   0.685081  0.489773   0.286591
            Sample_3   0.810637  0.006836   0.888038
            Sample_4   0.124098  0.347752   0.954853
            ```
            Annotation data
            ```
                 Sample_Name  Type
            0    Sample_0     Benign
            1    Sample_1     Pathologic
            2    Sample_2     Benign
            3    Sample_3     Benign
            4    Sample_4     Pathologic
            ```
        
        4. `Train model`
            ```bash
            logloss_beraf train \
              --features <path_to_feature_table> \
              --features_max_num 10 \
              --min_beta_threshold 0.2 \
              --annotation <path_to_annotation_table> \
              --sample_name_column "Sample_Name" \
              --class_column "Type" \
              --output_folder <path_to_output_folder>
            ```
        
        5. `Apply trained model to independent dataset`
            ```bash
            logloss_beraf apply \
              --features <path_to_test_feature_table> \
              --model <path_to_trained_model>
              --output_folder <path_to_output_folder>
            ```
        
        
        
Keywords: model machine learning diagnostic panel methylation
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Programming Language :: Python
