grep error

[LRVH727]

Hi,

Thanks for this package. Unfortunately i get the error "[grep](grep: HES_hesin_diag.csv: No such file or directory)" when trying to run the read_OPCS or read_ICD10. I tried to run the example code:
ICD10_codes=c('E10','E11')
ICD10_records=read_ICD10(ICD10_codes)

I work from Rstudio Workbench.

Thanks

[hdg204]

Hi there,

Are you an Exeter user? The file HES_hesin_diag.csv is available to members of UK Biobank Application 103356.

If you are on application 103356, I can make sure you have access to the file. If you are not, you'll need to use the table exporter to generate the file yourself. I'll try and get a readme up on how to do that over the weekend.

[LRVH727]

Hi,

I'm not sure, how do i know whether I'm an exeter user or on which application I'm on?
I have acces through the account of my supervisor.

[hdg204]

If you're not sure if you're at the University of Exeter, you probably aren't. I'll put up a readme later on how to generate the files you need, I wasn't aware anyone from outside of Exeter was looking at this!

[LRVH727]

Ahh University of Exeter! No, I'm not ;)
Awesome, looking forward to the readme.

[hdg204]

Hi LRVH727,

I've added a new section to the bottom of the readme which tells you how to create the files for the HES records. This should enable the use of read_ICD10 and read_OPCS.

The GP and death records can be extracted with a similar procedure. Cancer and self-report data is a bit of a pain because UKBB stores them in a wide format rather than a long format, for reasons known only to them.

You're the first non-Exeter person that's attempted this, so I hope my readme can be followed! You will need to change the file IDs (the system dx download commands at the top of the R script) because they will generate differently for you.

[LRVH727]

hi hdg204

Your readme works! I've only tried for the OPCS, ICD10 and ICD9 because that's all i need. I suspect it'll work for other records as well.

Many thanks