incorporate some additional phenotype variables that are not included here: https://github.com/dnanexus/UKB_RAP/blob/main/end_to_end_gwas_phewas/get-phewas-data.ipynb
I am using these tutorials:
https://github.com/dnanexus/UKB_RAP/blob/main/end_to_end_gwas_phewas/get-phewas-data.ipynb
https://saigegit.github.io/SAIGE-doc/docs/Installation_docker.html
https://documentation.dnanexus.com/science/scientific-guides/saige-gwas-walkthrough
and want to include APOE*4 dosage, APOE*2 dosage, and UKB assessment center in addition to the fields I currently have in my .phe file, which I generated using this tutorial: https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/gwas-ex
thank you!
Comments
6 comments
To kickoff this topic, yes, in the get-phewas-data.ipynb notebook, you will need to either specify field id(s) which correspond to desired UKB assessment center data or (in my understanding) retrieve/compute dosages for the APOEs and store them in form of text file. I am not sure if APOE gene dosages are directly available as field id.
I could be wrong, so other ideas here would be helping a lot!
Hi Ondrej,
Thank you so much for your reply! I had a similar thought, but couldn't find any documentation on retrieving APOE dosages or the field ID for the UKB assessment center.
Any additional ideas would be much appreciated!
@Anastazie Sedlakova? might know about APOE dosages.
My understanding is that you would need to extract dosages from geno data. You maybe get some pointers from here: https://community.dnanexus.com/s/question/0D582000000QjfmCAC/query-of-the-week-7-about-linking-geno-and-pheno-data
When you say "UKB assessment center", do you mean the whole big category? I mean https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=100000
If so, that would be a super large number of field ids to be included.
I am specifically interested in the location where individuals were seen, which I believe I located here: https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=54 ! Thank you for providing the link.
Yes, that sounds good. Let me than know if that worked, I am also interested to know this.
Please sign in to leave a comment.