Loading PGC data in tranSMART

[Paula]

Hi there,

Any idea if it is possible to load PGC data (http://www.med.unc.edu/pgc/) in tranSMART? I'm using tranSMART version 16.2 with Postgres.

The data is in the following tab-separated format (the first line is the header of the file, followed by the actual values per SNP):

snpid hg18chr bp a1 a2 or se pval info ngt CEUaf

rs3131972 1 742584 A G 1.0142 0.0354 0.7677 0.1783 0 0.1065

rs3131969 1 744045 A G 1.0985 0.0466 0.8491 0.1235 0 0.1382

More about the format can be found here: http://www.med.unc.edu/pgc/results-and-downloads

Would this kind of data map to any of the supported data types in the current tranSMART data model?

Thanks!

[Natalia Boukharov]

Hello Paula, 

SNP data can be loaded into transmart in VCF format. Here is the link to loading instruction using tMDataLoader https://github.com/Clarivate-LSPS/tMDataLoader/wiki/08.-Gene-Variant-Data-(vcf)

Copy number variation format is designed for aCGH data. Here is example https://github.com/Clarivate-LSPS/tMDataLoader/wiki/09.-aCGH-Data.

There is also variant data format and loading for using PLINK plugin https://github.com/Clarivate-LSPS/tMDataLoader/wiki/12.-PLINK-data.

Best,

Natalia

[Paula]

Hi Natalia,

Thank you for the links!

By looking at the links and documentation, it appears though that it is a requirement to have subject level data. Is this correctly understood? 

The PGC data doesn't include subject level results, but rather a summary for each SNP.

Any way of loading such summary data in tranSMART?

Thank you again!

[Natalia Boukharov]

I have looked at the "SCZ credible casual SNP" data file. Sorry, I did not realize that you are looking to load analysis results. You probably need to load this as GWAS. Here is a video:

https://www.youtube.com/watch?v=LNhvZ3ljT1Y

I don't have personal experience with this data. I believe, Rancho people worked with Pfizer to develop this feature: http://www.ranchobiosciences.com/contact/

https://github.com/hberube

[Paula]

That sounds promising, I will have a look at loading as GWAS. Thanks Natalia!