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

Release Notes

0.6.1

Bug fixing. Added new command lien argument to filter which models to use when running SMultiXcan.sh

0.6.0

This version includes the first release of MulTiXcan and S-MulTiXcan methods. It adds a minimalistic implem entation of PrediXcan that supports naive adjusting for covariates.

• Added --gwas_file option to input a single GWAS file.
• Addressed a plethora of edge cases in malformed input GWAS files.
• MetaXcanUI.py is no longer supported, and left for reference purposes.

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.