This mode compares the distribution of each feature used in a set of specific biomarker models. Distribution differences are quantified for feature signal between two sample sets (i.e., training set vs. validation set). A P-value (Kolmogorov-smirnov) and ratio of rank statistics is evaluated for each feature in each model processed.

It is implemented by

Mode Parameters

The following options are available in this mode

Flag Arguments Required Description
--maqcii-properties-file maqcii-properties-fileyes The maqcii properties file such as
--model-conditions-filemodel-conditions-fileyesThe model-conditions-file such as ‘model-conditions.txt’
--models-dirmodels-diryesThe directory containing models (may be within sub-directories)
--model-listmodel-listnoThe models to process (or ‘all’ to process all models). Comma separated, such as ‘DUDTR,YTNJM’. (default: all)
--model-exclude-listmodel-exclude-listnoThe models to NOT process (or ‘none’ to process all models). Comma separated, such as ‘DUDTR,YTNJM’. (default: none)
--signal-quality-calc-class signal-quality-calc-classyesFully qualified classname for an AbstractSignalQualityCalculator class
--eval-dataset-rooteval-dataset-rootnoThe eval-dataset-root directory or specify ‘-‘ to use the dataset-root directory specified in the model-conditions file (default: -)
--properties-training-labelproperties-training-labelnoThe label used to denote training values in the properties file. (default: training)
--properties-validation-label properties-validation-labelnoThe label used to denote validation values in the properties file. (default: validation)
--extended-output extended-outputyesIf true, extra output will be included. (default: false)
--merge-classesmerge-classesyesIf true, all classes will be merged. (default: false)
--max-num-classesmax-num-classesyesThe maximum number of classes (for the output file header) (default: 2)