z deprecated GUI Reference
This UI is no longer maintained and possibly broken.
MetaXcan's GUI is a wrapper around the command line tools. It is a trimmed down version of the most frequent usage of MetaXcan's scripts, thus it depends on the existence of precomputed support statistics generated by M01_covariances_correlations.py (see command line reference) and a matching transcriptome model. Examples of these files can be downloaded following same instructions from the GUI tutorial.
The actual UI might look a bit different from system to system, and version to version.
The GUI admits a setting of either Odd Ratio, Beta, or Sign of Beta, but not both at the same time.
| Parameter | Description | | ------------- | --------------- || GWAS file name pattern | Optional. This is a regular expression to filter file names from the input gwas folder (since it might contain, for example, documentation files). You can use it to select a single file too. | | separator | Character separator between columns in input files. Leave blank if your files are separated by any whitespace. | | SNP id | Name of column in input files containing SNP id. | | Reference Allele | Name of column in input files containing reference(other) allele. | | Effect Allele | Name of column in input files containing effect allele. | | Odd Ratios | Name of column in input files containing Odd Ratio values. | | Beta | Name of column in input files containing beta values. | | Beta sign | Name of column in input files containing sign beta values. | | P Value| Name of column in input files containing sign beta values. | | GWAS data folder | Path were GWAs data is to be loaded from. | | Processed beta folder | Path were processed betas will be written too. These are internal calculations. | | Weight Model DB | File containing the transcriptome model. | | Covariance | File were covariance matrices are stored. | | output file | File where the results will be output. |