fedpydeseq2-datasets 0.1.0

This package contains utilities to process TCGA data for fedpydeseq2.

Datasets organisation

This directory contains the data, assets and scripts necessary to:

• download the raw data necessary to run the tests and experiments, when not available in the repository, in the download_data directory;
• open the data when performing a Substra experiment in the assets directory;
• store the data in the data directory.

Data download

For a detailed description of the data download process, please refer to the README.

If you want to run the pipeline directly, you can use the script which is available in the distribution: fedpydeseq2-download-data

fedpydeseq2-download-data

By default, this script download the data in the data/raw directory at the root of the github repo.

To change the location of the raw data download, add the following option:

fedpydeseq2-download-data --raw_data_output_path <path>

If you only want the LUAD dataset, add the --only_luad flag.

You can pass the conda activation path as an argument as well, for example:

fedpydeseq2-download-data --raw_data_output_path <path> --conda_activate_path /opt/miniconda/bin/activate

Origin of the data

• The Counts_raw.parquet and recount3_metadata.csv files are downloaded from the RECOUNT3 database.
• The tumor_purity_metadata.csv file is downloaded from the Systematic pan-cancer analysis of tumour purity paper.
• The cleaned_clinical_metadata.csv file is downloaded from the An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics paper.

For more detailed references, see the References section.

Assets

The assets directory contains a TCGA opener necessary to open the data on each center when performing a federated experiment with Substra.

In particular, the fedpydeseq2_datasets/assets/tcga directory contains the following files:

assets/tcga
├── description.md
├── opener.py

The opener is a Python script that opens the data and makes it available to the Substra platform. The description.md file contains a description of the data.

For more details on how the opener works, please refer to the Substra documentation.

Raw data organisation

The data directory contains the raw data. The raw directory contains the data downloaded from the original sources, with the download_data scripts.

It is organized as follows:

data
├── raw
│   └── tcga
│       ├── <COHORT NAME>
│       │   ├── Counts_raw.parquet
│       │   └── recount3_metadata.csv
│       ├── centers.csv
│       ├── cleaned_clinical_metadata.csv
│       └── tumor_purity_metadata.csv

Data preprocessing

This module not only provides the raw data on which to test fedpydeseq2; it also provides the necessary preprocessing functions, to organise the data according to their center of origin, and to aggregate the raw data into metadata and counts acceptable to run pydeseq2 or fedpydeseq2.

These preprocessing function usually create the preprocessed data in a processed_data_path directory, with the following structure (the files shown below are created by different preprocessing functions).

└── <processed_data_path>
    ├── tcga
    │   ├── <COHORT NAME>
    │   │   ├── counts.parquet
    │   │   └── clinical_data.csv
    ├── centers_data
    │   └── tcga
    │       ├── <dataset_and_dge_experiment_id>
    │       │   ├── <center_i>
    │       │   │   ├── counts_data.csv
    │       │   │   ├── metadata.csv
    │       │   │   └── ground_truth_dds.pkl
    └── pooled_data
        └── tcga
            ├── <dataset_and_dge_experiment_id>
            │   ├── counts_data.csv
            │   ├── metadata.csv
            │   └── ground_truth_dds.pkl

These files are automatically generated, if they are not already present from the raw files or if the force option is on.

Note that the centers are always indexed by an integer, starting from 0. For example, one would have center_0,...,center_3 if there are 4 centers in the experiment.

The <dataset_and_dge_experiment_id> is an identifier of a differential gene expression task (and its specific hyperparameters) and a TCGA dataset. fedpydeseq2 or deseq2 can then be run on the data corresponding to that DGE task.

Details on the processed data

In this repository, we study the following cofactors:

• the gender of the patients, which is obtained from the cleaned_clinical_metadata.csv file;
• the CPE of the samples, which is obtained from the tumor_purity_metadata.csv file;
• the stage of the patients, which is obtained from the cleaned_clinical_metadata.csv file. this stage is originally a stage between I and IV, but we have grouped them into I-II-III (Non-advanced) and IV (Advanced) stages, to have a binary covariate.
• the center_id of the samples, which is obtained from the centers.csv file and used to create natural centers for the federated experiments.

The processing is done by functions in the fedpydeseq2_datasets directory. There are three main functions.

• the common_preprocessing_tcga function in the fedpydeseq2_datasets/common_preprocessing.py file;
• the setup_tcga_dataset function in the fedpydeseq2_datasets/process_and_split_data.py file;
• the setup_tcga_ground_truth_dds function in the tcga_preprocessing/create_reference_dds.py file.

The role of the common_preprocessing_tcga function is to generate counts and processed clinical data for a given cohort (e.g. LUAD), from the raw data.

└── processed
    ├── tcga
    │   ├── <COHORT NAME>
    │   │   ├── counts.parquet
    │   │   └── clinical_data.csv

The counts.parquet file contains the counts data, indexed by TCGA sample barcode, and with columns corresponding to the gene_id in ENSEMBL convention. Note that we filter out the PAR_Y genes, as they are not common to all patients. The clinical_data.csv file aggregates the different metadata from the different sources described above in a per-cohort fashion. This csv is indexed by the TCGA sample barcode. It contains the following columns:

• gender: the gender of the patient;
• CPE: CPE stands for "consensus measurement of purity estimations", and is an aggregate of different purity estimations for the sample;
• stage: the stage of the patient, as an integer between 1 and 4
• center_id: the center id of the sample, as an integer
• is_normal_tissue: a boolean indicating if the sample is a normal tissue or not.
• T : the tumor grade of the patient, as an integer between 1 and 4
• N : the nodal status of the patient, as an integer between 0 and 3
• M : the metastasis status of the patient, as an integer between 0 and 1

The role of the setup_tcga_dataset function and the setup_tcga_ground_truth_dds function is to generate the data necessary for the federated AND corresponding pooled experiments, creating this part of the arborescence:

└── processed
    ├── centers_data
    │   └── tcga
    │       ├── <dataset_and_dge_experiment_id>
    │       │   ├── <center_i>
    │       │   │   ├── counts_data.csv
    │       │   │   ├── metadata.csv
    │       │   │   └── ground_truth_dds.pkl
    └── pooled_data
        └── tcga
            ├── <dataset_and_dge_experiment_id>
            │   ├── counts_data.csv
            │   ├── metadata.csv
            │   └── ground_truth_dds.pkl

The <dataset_and_dge_experiment_id> identifies an experiment. It concatenates not only the dataset name (TCGA cohort), but also the design factors, continuous factors as well as other parameters used to filter the data. The counts_data.csv file contains the counts data, indexed by TCGA sample barcode, and with columns corresponding to the gene_id in ENSEMBL convention. The metadata.csv file contains the clinical data, indexed by the TCGA sample barcode, and containing only the columns corresponding to a design factor. The ground_truth_dds.pkl file contains the ground truth for the differential expression analysis, as a dds object from the DESeq2 package.

For more details on these functions, please refer to their respective documentations.

Note: the setup_tcga_dataset function will binarize the stage into two categories: Advanced and Non-advanced. Advanced corresponds to stage IV, and Non-advanced corresponds to stages I, II and III. For the TCGA-PRAD cohort, we do not have the stage information, but we infer the stage from the T, N and M columns. If the N or M columns are > 0, the stage is IV (see the following reference) and hence the Advanced stage. Otherwise, it is Non-advanced.

References

The data downloaded here has mainly been obtained from TCGA and processed by the following works.

[1] Aran D, Sirota M, Butte AJ. Systematic pan-cancer analysis of tumour purity. Nat Commun. 2015 Dec 4;6:8971. doi: 10.1038/ncomms9971. Erratum in: Nat Commun. 2016 Feb 05;7:10707. doi: 10.1038/ncomms10707. PMID: 26634437; PMCID: PMC4671203. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4671203/

[2] Jianfang Liu, Tara Lichtenberg, Katherine A. Hoadley, Laila M. Poisson, Alexander J. Lazar, Andrew D. Cherniack, Albert J. Kovatich, Christopher C. Benz, Douglas A. Levine, Adrian V. Lee, Larsson Omberg, Denise M. Wolf, Craig D. Shriver, Vesteinn Thorsson et al. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics, Cell, Volume 173, Issue 2, 2018, Pages 400-416.e11, ISSN 0092-8674, https://doi.org/10.1016/j.cell.2018.02.05 https://www.sciencedirect.com/science/article/pii/S0092867418302290

[3] Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL, Zhang D, Joseph L, Leek JT, Jaffe AE, Nellore A, Collado-Torres L, Hansen KD, Langmead B (2021). "recount3: summaries and queries for large-scale RNA-seq expression and splicing." Genome Biol. doi:10.1186/s13059-021-02533-6 https://doi.org/10.1186/s13059-021-02533-6, https://doi.org/10.1186/s13059-021-02533-6.