resources

Generate mapping from TopMed raw variables to TopMed harmonized variables

Contents

• map-topmed-raw-to-harmonized/

  • generate_mapping.py -- Script
  • raw-to-harmonized-topmed-vars.csv -- Output

• human_readable_harmonized_variable_documentation/

  • TopMED variable documentation

• merged_TOPMed_harmonized_data_file

Notes

• In order to run scripts that open Google spreadsheets, you need credentials in ~/.config/gspread/service_account.json.
  • Instructions: https://docs.gspread.org/en/v6.1.3/oauth2.html
  • Also load_data.py has a function for returning df from worksheet

External resources and generated CSV files

• harmonized-variable-documentation
  • Location of local clone of UW-GAC/topmed-dcc-harmonized-phenotypes. Clone that repo in the same directory as this repo, and the code that needs it should work.

short_name	local_path	web_location
From external source
biolincc_variables_all_studies	./resources/copies_of_external_source_files/biolincc_variables_all_studies.csv	https://drive.google.com/file/d/1I_xZWRDUMHmz7jTNUFaVAQALe0ruVg6i/view?usp=drive_link
dbgap_priority_V1	./resources/copies_of_external_source_files/dbgap_variables_priority_cohorts_V1.csv	https://docs.google.com/spreadsheets/d/1xe-aSFH0PJ_p1e4t5hEyDWlFwMYmV_6g8N8TD-izIEo/edit?gid=1719407279#gid=1719407279
dbgap_priority_V2	./resources/copies_of_external_source_files/dbgap_variables_priority_cohorts_V2.csv	https://docs.google.com/spreadsheets/d/1o5rHZMbv6oj1EDEmvXA5zT-Jr1zM5dKS/edit?gid=57103008#gid=57103008
dbgap_priority	./resources/copies_of_external_source_files/dbgap_variables_priority_cohorts_V2.csv	https://docs.google.com/spreadsheets/d/1o5rHZMbv6oj1EDEmvXA5zT-Jr1zM5dKS/edit?gid=57103008#gid=57103008
dbgap_priority_V3	./resources/copies_of_external_source_files/dbgap_variables_priority_cohorts_V3.csv	https://docs.google.com/spreadsheets/d/1U38yPQnazhLAQm-OadVujHyIqB4T50qG5BpSB7QvUkA/edit?gid=1179634079#gid=1179634079
picsure_dd	./resources/copies_of_external_source_files/picsure_data_dictionary.csv
topmed_harm_var_json_docs	../topmed-dcc-harmonized-phenotypes/harmonized-variable-documentation/	https://github.com/UW-GAC/topmed-dcc-harmonized-phenotypes/tree/master/harmonized-variable-documentation
aha_harmonized	./resources/copies_of_external_source_files/AHA_TABLES 1(Sheet1).csv
aha_study_vars	./resources/copies_of_external_source_files/AHA_TABLES 1(Sheet2).csv
bdchm_priority_not_in_topmed	./resources/copies_of_external_source_files/priorityPhvNotInTM_sheet.csv	https://docs.google.com/spreadsheets/d/1G-AIk2m4UCDfh1OvFID3bewQXqxExeKNNmVxaswLT8E/edit?gid=215586941
Generated CSVs
topmed_raw_to_harm	./resources/map-topmed-raw-to-harmonized/raw-to-harmonized-topmed-vars.csv
topmed_plus_dbgap	./resources/merged_TOPMed_harmonized_data_file/merged_variables.csv
topmed_not_dbgap	./resources/merged_TOPMed_harmonized_data_file/raw_to_harm_only.csv
dbgap_not_topmed	./resources/merged_TOPMed_harmonized_data_file/dbgap_priority_only.csv
aha_dbgap_picsure	./resources/aha_doc/aha_dbgap_picsure.csv

---