Posts
Error No intersection between model names in MetaXcan Results and Prediction Models
2021-07-23
Festus
𝕋his error happen when the strings captured from the metaxcan results and models don’t coincide
A good example is when the metaxcan results' captured names looked like Aorta while the models' captured names looked like Artery_Aorta, this will result into this error
[…] …
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BrainXcan Brain Feature Prediction Models
2021-07-22
Yanyu Liang
𝕊-BrainXcan takes GWAS as input and return the association between GWAS phenotype and a list of brain image-derived phenotypes.
BrainXcan manuscript link.
Software documentation (Quick start) link.
BrainXcan database link.
Analysis scripts link.
[…] The software is built upon both Python and …
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I need help and these FAQ doesn't cover my issue!
2021-07-21
PredictDB Team
𝔸: You can ask questions at the Google Group: predixcanmetaxcan@googlegroups.com
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AttributeError 'NoneType' object has no attribute 'groups'
2021-07-21
Festus
𝕋his error happens when using the Multixcan tool, it usually happens when the tool cant find files in the Metaxcan folder you provided. Thus halting the process of meta analyzing the results. The most probable cause of this error are;
[…] –metaxcan_filter …
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Can I predict genes on chromosome X or Y?
2021-07-21
PredictDB Team
ℕot at the moment. Sex chromosome genes need to be handled differently than those on the autosomes, and do not fit into our existing analysis pipeline.
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Error low % of SNPs used
2021-07-21
Festus
𝕋here are different reasons where you could get a low % of SNPs in the model used with your individual level data or summary stats file. Some of the issues include;
[…] Little overlap between the model SNPs and genotype/summary stats SNPs
[…] Incomplete/malformed models .db file …
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GTEx v8 models on eQTL and sQTL
2021-07-21
PredictDB Team
𝕎e have produced different families of prediction models for sQTL and eQTL, using several prediction strategies, on GTEx v8 release data.
We recommend MASHR-based models below. Elastic Net-based are a safe, robust alternative with decreased power.
[…] Expression and splicing prediction models …
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How can I build my own prediction model?
2021-07-21
PredictDB Team
𝔽or elastic net models, you can find a tutorial here(https://github.com/hakyimlab/PredictDB-Tutorial)
The newer GTEx v8 models were generaed with code available here. The documentation is still a work in progress, don’t hesitate to use the PrediXcan/MetaXcan Google Group to ask for support. …
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How do I query the prediction model db?
2021-07-21
PredictDB Team
𝕋he .db files are simple sqlite files. You can programmatically query them via python, R, perl, etc (using appropriate libraries). Find example queries in this link(https://github.com/hakyimlab/PrediXcan/blob/master/Software/query-db.Rmd)
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How was the covariance data calculated?
2021-07-21
PredictDB Team
𝔽or the GTEx models, we calculated the covariance of the SNP dosages within our training (GTEx) samples. For the DGN model, we used public genotype data from 1000 Genomes to calculate the covariance of the SNP dosages.
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