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Here you will find several articles that might help you getting up and running, or troubleshoot common issues.

Release Notes

0.5.0

This version is a major overhaul of the main MetaXcan analysis tools. The GWAS parsing engine was repurposed using pandas. MetaXcan calculation was optimized. We observed runtime decreases between 30% and 60%. Many command line argument changes.

*"--weight_db_path" changed to "--model_db_path" in MetaXcan.py, M03_betas.py, M04_zscores.py, MetaMany.py *MetaXcan no longer writes intermediate statistics, and now works entirely in memory. This means that the "--beta_folder" in MetaXcan.py is no longer available. If you need these stats, they are still available from M03_betas.py.

• "--compressed_gwas" argument was dropped. Now gzip compression or flat file status is inferred from the file name. i.e. files ending with common gzip extensions will be assumed to be compressed.
• "--scheme", "--zscore_scheme", "--normalization_scheme", "--selected_dosage_folder" arguments were dropped.
• "--overwrite" optional argument was added. If set at the command line parameters, the results file will be overwritten if it exists.
• "--beta_zscore_column" renamed to "--zscore_column"
• Pandas module is now a dependency. Please install it if it is not yet part of your environment.
• Results file header is now all lower case.

0.3.3

• Updated MetaMany.py
• Command line parameter changes
• Refactor to support new features

0.3

• Fixed bug fore --zscore_column parameter, where signs wouldn't be flipped when GWAS and transcriptome model didn't agree on effect allele.
• Support for new PredictDB database format. (more info on this soon)
• New output parameters: prediction performance pvalue, prediction performance qvalue, MetaXcan association effect size.
• A swarm of tiny usability improvements across all scripts.