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MetaXcan software and manuscript
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how to get predicted expression level,Tg? #149

Open ymqwa opened 2 years ago

ymqwa commented 2 years ago

Hi, I have GWAS summary data and individual level data in the same cohort, also have DNA methylation prediction models. I use GWAS summary data to run Predict.py, get the methylation-level association results. Now i want to get the predicted methylation value, just like predicted expression Tg . i dont know if it can be got ? and if can , how to do ?

Thank you, best mqyang.

Fnyasimi commented 2 years ago

have a look at this for individual level data and this for summary stats.

I hope this helps

ymqwa commented 2 years ago

Really appreciate! @Fnyasimi

but when i run Predict.py, I got the following output: INFO - Loading samples INFO - Loading model INFO - Preparing genotype dosages INFO - Setting whitelist from available models INFO - Processing genotypes INFO - Preparing prediction INFO - Couldn't import h5py_cache. Anyway, this dependency should be removed. It has been folded into h5py Level 9 - Processing vcfs Level 9 - Processing vcf chrall_qc_3.vcf.gz Traceback (most recent call last): File "/Public/xyzhao/data/methylation/metaxcan/MetaXcan-master/software/Predict.py", line 270, in run(args) File "/Public/xyzhao/data/methylation/metaxcan/MetaXcan-master/software/Predict.py", line 198, in run results.update(gene, dosage, weight) AttributeError: 'NoneType' object has no attribute 'update'

Here is my code: conda activate MetaXcan /Public/software/MetaXcan/Predict.py \ --model_db_path methylation_r01_FHS.db \ --vcf_genotypes chrall_qc_3.vcf.gz \ --vcf_mode genotyped \ --prediction_output methy_predict.txt \ --prediction_summary_output methy_predict_summary.txt \ --verbosity 9 \ --throw

i don't know how to fix it. Would you have any thoughts on that? Looking forward to your reply best mqyang.

DoraCChen commented 2 years ago

Hi, I also had a similar question -

Since Summary-PrediXcan directly computes the gene-level association results from summary GWAS data, is there any way to derive and output predicted gene expression level Tg? I know that for individual-level PrediXcan it is possible to get Tg output using the Predict.py script, but the association analyses are different between individual and summary-level PrediXcan. How can we extract this information? I looked through the wiki page that was linked for S-PrediXcan but wasn't able to find the relevant information.

hakyim commented 2 years ago

Unfortunately, the individual level information cannot be recovered from the summary statistics. To calculate Tg for a set of individuals, you will need their genotype data. You can use your own cohort's genotype data and apply the individual level predixcan prediction software predict.py or use a reference genotype such as 1000G or others. I hope this helps Haky

On Mon, Apr 4, 2022 at 1:11 PM Dorothy Chen @.***> wrote:

Hi, I also had a similar question -

Since Summary-PrediXcan directly computes the gene-level association results from summary GWAS data, is there any way to derive and output predicted gene expression level Tg? I know that for individual-level PrediXcan it is possible to get Tg output using the Predict.py script, but the association analyses are different between individual and summary-level PrediXcan. How can we extract this information? I looked through the wiki page that was linked for S-PrediXcan but wasn't able to find the relevant information.

— Reply to this email directly, view it on GitHub https://github.com/hakyimlab/MetaXcan/issues/149#issuecomment-1087861794, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAW2ROMNQH5J57UOHESQRTTVDMWDZANCNFSM5R27ORWQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>