FAQ

FAQ

Error for region (...) LinAlgError('SVD did not converge')

2021-07-23 PredictDB Team
𝕆ne step of the summary imputation, the computation of snp covariance matrix inverse, is performed via singular value decomposition (SVD). Numerical solutions to the SVD algorithm are not guaranteed to converge, and fail on some regions. When this happens, unmeasured zscores will not be present in … Read more →
FAQ

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 […] … Read more →
FAQ

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 … Read more →
FAQ

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. Read more →
FAQ

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 … Read more →
FAQ

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. Read more →
FAQ

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) Read more →
FAQ

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. Read more →
FAQ

How was the expression data preprocessed for training the prediction models?

2021-07-21 PredictDB Team
𝔸: We used the expression pre-processed by the GTEx analysis working group. Covariates are the same as used in the eQTL analysis. GTEx processing pipeline is here(https://github.com/broadinstitute/gtex-pipeline/), and Docker image is here(https://hub.docker.com/r/broadinstitute/gtex_eqtl/). -[ ] … Read more →
FAQ

Q: Are performance measures of prediction available?

2021-07-21 PredictDB Team
𝔽or elastic net models, they can be found in the extra table in each sqlite db. The mashr-based models which use fine-mapping for variable selection, the performance measures are not available. You can use the elastic net performance as a proxy. Read more →