How to perform an exploratory data analysis

To explore preprocessing, encodings and/or reports without running a machine learning algorithm, the ExploratoryAnalysis instruction should be used. The components in the definitions section are defined in the same manner as for all other instructions (see: How to specify an analysis with YAML, for importing a dataset see How to import data into immuneML).

The instruction consists of a list of analyses to be performed. Each analysis should contain at least a dataset and a report. Optionally, the analysis may also contain an encoding along with labels if applicable. In the example below, two analyses are done:

• my_analysis_1 runs report my_seq_lengths directly on dataset my_dataset

• my_analysis_2 first encodes my_dataset using my_regex_matches before running report my_matches.

  exploratory_analysis.yaml

  definitions:
    datasets:
      # imported datasets
      my_dataset: # user-defined dataset name
        format: AIRR
        params:
          metadata_file: path/to/metadata.csv
          path: path/to/data/
  
    encodings:
      my_regex_matches:
        MatchedRegex:
          motif_filepath: path/to/regex_file.tsv
  
    reports:
      my_seq_lengths: SequenceLengthDistribution # reports without parameters
      my_matches: Matches
  
  instructions:
    my_instruction: # user-defined instruction name
      type: ExploratoryAnalysis
      analyses:
        my_analysis_1: # user-defined analysis name
          dataset: my_dataset
          report: my_seq_lengths
        my_analysis_2:
          dataset: my_dataset
          encoding: my_regex_matches
          report: my_matches
  

Where the file regex_file.tsv must be a tab-separated file, which may contain the following contents:

id	TRB_regex
1	ACG
2	EDNA
3	DFWG