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 →

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 →

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 … Read more →

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 →

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 →

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 →

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 →

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 →

𝕋his can be found in the sample_info table in each sqlite db. -[ ] TODO check that this info is available in the newer models. For GTEx V8 models, only European samples were used to match the GWAS study LD better. See list here Sample size by tissue Read more →

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