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proteomics

README.md

Proteomics analysis examples

This folder contains 2 examples of analyses using public proteomics data for demonstration purposes.

File structure

Folder Description
protein_DE_analysis Folder containing jupyterlab notebooks to run differential expression analysis on the UKB-RAP.
protein_pQTL Folder containing a notebook to prepare the data to input into the REGENIE app on the UKB-RAP.

How to extract proteomics data from UKB-RAP

The proteomics data on UKB-RAP is available in the Cohort Browser. There are 2 options for extracting the data:

  1. Use the dx extract_dataset command line tool. An example for how to do this can be found in the 0_extract_phenotype_protein_data.ipynb notebook.
  2. Use the Table exporter app on the platform. To use this tool you'll need to specify the following input params:

Dataset or Cohort or Dashboard: <file path to the cohort dataset or .dataset file in the root directory>

File containing Field Names: If you want to use all proteins then use field_names.txt

Entity: Options are olink_instance_0, olink_instance_2, olink_instance_3 depending on the samples you want to include. See UKB showcase and UKB-PPP preprint for more information on the difference in samples included in the different datasets.