Posts

Protein prediction models - ARIC

2022-11-14 Sabrina Mi
𝔸RIC protein prediction models in predictdb format can be downloaded from here https://uchicago.box.com/s/3sf4y4gv6c7zam0l5fxicpcd3zji5wzc See more details here https://lab-notes.hakyimlab.org/post/2021/09/08/generating-metaxcan-prediction-model-from-aric-pwas/ Read more →
FAQ

MetaXcan output file formats

2022-03-08 Festus
𝕋he MetaXcan Software hosts a suite of tools i.e PrediXcan, SPrediXcan, MultiXcan and SMultiXcan. This post describes the file format output from each tool. […] Individual-level data method to compute gene-trait associations. Detailed info The output is a tab delimited file which contains … Read more →

Protein prediction for trait mapping in diverse populations

2022-02-12 Ryan Schubert, Heather Wheeler
ℙrediXcan ready databases and covariance files of the paper “Protein prediction for trait mapping in diverse populations” can be downloaded from here https://doi.org/10.5281/zenodo.4837327 Read more →
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 →

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 … Read more →

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 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 →