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.

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