Re: [PrediXcan/MetaXcan] PrediXcan, DGN DB, snp details?

[Scott Dickinson]

Hi Bin Ye,

We have just uploaded files for the list of snps used for each model.

This should have all the info you're looking for to use the DGN model: https://s3.amazonaws.com/imlab-open/Data/PredictDB/hapmapSnpsCEU.tar.gz

Best,

Scott

On Mon, Nov 14, 2016 at 10:39 AM, Bin Ye <robi...@gmail.com> wrote:

Hi,

Thank you for making a great tool like predixcan! I'm trying to use DGN DB to impute gene expression for our dataset (which contains imputed 1kg SNPs), however there's ~20% of DGN DB snps (by matching rsids) not presented in our dataset. I would like to dig deeper to find out what cause the discrepancy. But I can't extract the chromosomal locations from the DGN DB file, could you please let me know which hapmap SNP db files were using to generate the DGN DB? 

Thank you very much!

Bin

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[farnush farhadi]

Hi, 

As one of the files in DGN-WB_0.5.db, there is a construction.csv. Could you please guide me on how can I generate this for my study? (can I use yours?)

Cheers,

Farnush 

On Monday, November 14, 2016 at 3:01:50 PM UTC-8, Scott Dickinson wrote:

Hi Bin Ye,

We have just uploaded files for the list of snps used for each model.

This should have all the info you're looking for to use the DGN model: https://s3.amazonaws.com/imlab-open/Data/PredictDB/hapmapSnpsCEU.tar.gz

Best,

Scott

On Mon, Nov 14, 2016 at 10:39 AM, Bin Ye <robi...@gmail.com> wrote:

Hi,

Thank you for making a great tool like predixcan! I'm trying to use DGN DB to impute gene expression for our dataset (which contains imputed 1kg SNPs), however there's ~20% of DGN DB snps (by matching rsids) not presented in our dataset. I would like to dig deeper to find out what cause the discrepancy. But I can't extract the chromosomal locations from the DGN DB file, could you please let me know which hapmap SNP db files were using to generate the DGN DB? 

Thank you very much!

Bin

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[Scott Dickinson]

Hi Farnush,

The construction table in each PredictDB database contains the random seed that was used to partition the samples when doing 10-fold cross validation. It is included in the database only for reproducibility purposes should anyone need to reconstruct the models.

If you’d like to see the whole model creation process, check out https://github.com/hakyimlab/PredictDBPipeline

Scott

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[farnush farhadi]

Hi Scott, 

Thank you for your answer. 

Cheers,

Farnush 

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Farnush Farhadi, M.Sc.
Dr. Sara Mostafavi’s Lab
Centre for Molecular Medicine and Therapeutics (CMMT)
University of British Columbia | Child & Family Research Institute
980 West 28th Avenue, Room 3109 | V5Z 4H4, Vancouver, BC, Canada

"Logic will get you from A to B. Imagination will take you everywhere" Albert Einstein