I want to run a PheWAS analysis using PHESANT and currently trying to generate the phenotype file. I am using table exporter to extract the phenotype data for my variables of interest.
My input is the entire phenotype dataset, and a field names text file (with 1000s field names, such as p30630_i0, etc).
The output file I am getting has columns corresponding to each phenotype variable (in UKB format), but I would like an additional column with the participant IDs. I am not sure what input I need to include so that I get the participant IDs.
Thanks!
'eid' is the correct field name for participant ID, but something is wrong with Table Exporter. I have let DNAnexus product team know.
There are three ways that you can solve this issue meanwhile.
1) You can extract the entire pheno dataset and filter for the field you want yourself. Run the Table exporter with no input in Field title, field name, and a file containing field name would give you entire dataset.
Hi, this bug is still present and a fix would be appropriate. I cannot export data containing the EID without FIRST finding this thread or reading the troubleshooting guide on a page that was not immediately relevant to me using `dx run table-exporter` and not the GUI. To explain why this is frustrating: Following the documentation on how to export data using the table-exporter, it is problematic that this is only mentioned in the trouble shooting guide, since exporting data with the id column is the most basic functionality of this app. Users (I, at least) expect that to work without any additional work-around. So in my example, I had small export jobs running indefinitely for several days (which costs money!), because this bug does not cause a job to terminate, but to just run forever (!). This is not OK and I would appreciate an update on this.
Comments
7 comments
It should call "eid" field. Can you try if that is working with just a few field as a test?
Table exporter failed when I tried calling "eid"
'eid' is the correct field name for participant ID, but something is wrong with Table Exporter. I have let DNAnexus product team know.
There are three ways that you can solve this issue meanwhile.
1) You can extract the entire pheno dataset and filter for the field you want yourself. Run the Table exporter with no input in Field title, field name, and a file containing field name would give you entire dataset.
2) You can use dx extract_dataset instead.
https://github.com/dnanexus/OpenBio/blob/master/dx-toolkit/dx_extract_dataset_bash.ipynb
https://documentation.dnanexus.com/user/helpstrings-of-sdk-command-line-utilities#extract_dataset
3) If you have done data extraction using dxdata in Jupyternotebook https://github.com/dnanexus/OpenBio/blob/master/UKB_notebooks/ukb-rap-pheno-basic.ipynb that has Spark enable, you could still do that. However, if you have not done this before, we recommend that the proper method is to use dx extract_dataset.
The engineers figure out what's going on. The eid present in multiple data, so it crash when we request it without specify which data we want.
You can specify "entity" of the app as "participant" and then request for eid together with other field. I have tried it, and it works.
@Niyati Jain? I misspell participant earlier. Just FYI.
Thanks @Chai Fungtammasan? ! I was able to get the table with participant ID table
Hi, this bug is still present and a fix would be appropriate. I cannot export data containing the EID without FIRST finding this thread or reading the troubleshooting guide on a page that was not immediately relevant to me using `dx run table-exporter` and not the GUI. To explain why this is frustrating: Following the documentation on how to export data using the table-exporter, it is problematic that this is only mentioned in the trouble shooting guide, since exporting data with the id column is the most basic functionality of this app. Users (I, at least) expect that to work without any additional work-around. So in my example, I had small export jobs running indefinitely for several days (which costs money!), because this bug does not cause a job to terminate, but to just run forever (!). This is not OK and I would appreciate an update on this.
Please sign in to leave a comment.