FAQ

FAQ

Q: How many samples were used to train each model?

2021-07-21 PredictDB Team
𝕋his can be found in the sample_info table in each sqlite db. -[ ] TODO check that this info is available in the newer models. Read more →
FAQ

There is an awful lot of models! Which ones should I use?

2021-07-21 PredictDB Team
𝔸1: GTEx v8 MASHR-based models are parsimonious and have been shown to yield more reliable set of putative causal variants. These are the best option. However, they require GWAS preprocessing on older GWAS as detailed here. A2: GTEx v8 UTMOST models are a robust but with lower performance. These are … Read more →
FAQ

Unexpected error: No objects to concatenate

2021-07-21 Festus
𝕋his error raise when the multixcan tool does get gwas files which should be concatenated. The error is common when you are provoding multiple gwas files in a directory. The common mistake that brings the issue rises from; […] –gwas_file_pattern “(.*).txt” #selects all gwas … Read more →
FAQ

Unexpected error: nothing to repeat at position 0"

2021-07-21 Festus
𝕋his error happens when the data bases cannot be loaded into the tool and the main cause might be; […] –models_name_pattern “en_(.*).db” –models_name_filter “en_Brain_(.*).db” Read more →
FAQ

What do i do with these models?

2021-07-21 PredictDB Team
𝕋hese models allow prediction of gene expression or alternative splicing on a GWAS study. The predicted levels can be associated to a complex trait such as a disease’s susceptibility. PrediXcan implementation uses these models and individual-level data. MetaXcan repository contains an … Read more →
FAQ

What does “TW_” mean in the GTEx v6 file names?

2021-07-21 PredictDB Team
𝕋his is an abbreviation for “Tissue-Wide.” We have historically created a Cross-Tissue model, which is a measure of the expression common across all tissues, and Tissue-Specific models (TS), which is modeled as an orthogonal component to the shared cross tissue component. Details can be found … Read more →
FAQ

Why are there fewer available genes/introns in the prediction models than in the GTEx dataset?

2021-07-21 PredictDB Team
𝕋he prediction model databases only contain models that pass a stringent criteria (each family of models has its own criteria, e.g. MASHR models require at least one snp with high posterior probability of being an eQTL). Our model training algorithms are complex and conservative. Sometimes, a good … Read more →
FAQ

Error 0% SNPs used

2021-07-20 Festus Nyasimi
𝕋his error usually occurs when there is a mismatch between the SNP ids used in the model and those used in the genotype file or the summary stats file. A few examples to mention; 1. Using rsids in the models against variant ids (chr_pos_ref_alt_build) in the genotype and summary stats file and vice … Read more →