How to extract hospital inpatient and death data using table exporter?
Using table exporter, I am trying to extract phenotype data plus the main HES table and death registry data to my project… I'm following this UKB-RAP notebook (https://github.com/UK-Biobank/UKB-RAP-Notebooks-Access/blob/main/RStudio/A110_Export_participant_data.Rmd) for the phenotype data which seems to be working… is it possible to adapt this to extract HES & death data too?
I know I need to change the entity to ‘hesin’ instead of ‘participant’, but beyond that I'm lost. Any suggestions or alternative ways (preferably with a structured walk through…) of extracting HES & death (using the GUI).
Thanks
Comments
2 comments
Hi Lewis,
There are instructions on this DNANexus page on how to use Table Exporter:
https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/accessing-data/accessing-phenotypic-data#create-a-tsv-or-csv-file-using-table-exporter
including entering the 'Entity’ string under Inputs > Advanced Options, which will be the name of your data table of interest, e.g. hesin.
I hope that helps.
Many thanks,
Catherine
Hi Lewis,
I found a R package authored by Icpilling might be useful for your question: lcpilling/ukbrapR: R package for working in the UK Biobank Research Analysis Platform (RAP) (github.com). Hope that may help you.
Best regards,
Yueqi Chen (Jackie)
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