Former User of DNAx Community_13

Are the PLINK files (.bed, .bim, .fam) available for use from the 200k whole genomes? At https://biobank.ndph.ox.ac.uk/showcase/field.cgi?tk=WfgiZClxpHlEjcBY9XYOIUP5JMWR5Tr9259499&id=24305, it notes that these data are "restricted"?

I had thought that the 200k whole genome data were now available for use, so I assumed that included the PLINK files. Thanks!

• Former User of DNAx Community_13
• 08 November 2022 00:00
• 1 follower
• 1 comment
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Thanks Chai! I'm encountering an odd issue setting up a Docker image, when trying to build on top of the r-base image, I get the following error:  

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• 09 September 2022 17:11
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Is there a way to run an R script with a specified environment (snapshot) and instance type?

• Former User of DNAx Community_13
• 03 September 2022 00:00
• 2 followers
• 4 comments
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To clarify - a way to run an Rscript from bash terminal in RAP.

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• 02 September 2022 22:09
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@Ondrej Klempir? that solution didn't work for me, please see the attached image. Am I missing something? 

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• 05 August 2022 23:35
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I forgot to say - I'm using the exome data from the 450k release (the updated release is still refreshing in my project).

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• 29 July 2022 18:55
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So far I'm just looking at whether any ICD10 codes from the summary diagnoses are significantly associated with some exonic variants in a gene of interest. I am planning to try PHESANT in the futur...

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• 29 July 2022 18:54
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When I generate a new file in a JupyterLab notebook and upload it to my project storage, I cannot access that file in the same session, even if I refresh. I get the error that the file does not exist.

In order to access these files, I have to terminate my current JupyterLab session and start a new one, which is time consuming. Is there a workaround I'm not aware of? Thanks!

• Former User of DNAx Community_13
• 29 July 2022 00:00
• 1 follower
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Thanks Ondrej, I was able to install devtools after following what you did. Thanks! I still had to do some additional steps to facilitate installation of the PheWAS package, which I'll outline here...

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• 28 July 2022 21:57
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