Study folder format

When loading a study structure to TMTK a folder format is expected, the same structure is supported in transmart-batch.

File structure

study_directory
├── study.params
│
├── clinical
│   ├── clinical.params
│   ├── column_mapping.txt
│   ├── word_mapping.txt
│   ├── modifiers.txt
│   ├── ontology_mapping.txt
│   ├── trial_visits.txt
│   ├── data_file_1.txt
│   ├── ...
│   └── data_file_X.txt
│
├── expression
│   ├── annotation
│   │       ├── mrna_annotation.params
│   │       └── mrna_annotation_file.txt
│   ├── mrna.params
│   ├── subject_sample_mapping.txt
│   └── expression_data_file.txt
│
├── ...
│
├── rnaseq
│   ├── annotation
│   │       ├── rnaseq_annotation.params
│   │       └── rnaseq_annotation_file.txt
│   ├── rnaseq.params
│   ├── subject_sample_mapping.txt
│   └── rnaseq_data_file.txt
│
└── tags
    ├── tags.params
    └── tags.txt

Study parameters

A parameter file in which the study wide parameters are stored like the study identifier and whether a study needs to be securly loaded.

  • STUDY_ID Mandatory Identifier of the study.
  • SECURITY_REQUIRED _Default:_ Y. Defines study as Private (Y) or Public (N).
  • TOP_NODE The study top node. Has to start with ‘' (e.g. ‘\Public Studies\Cell-lines’). Default: ‘\(Public|Private) Studies\<STUDY_ID>’.