viprs_evaluate

Evaluate Predictive Performance of PRS (viprs_evaluate)

The viprs_evaluate script is used to evaluate the performance of the PRS predictions using the PRS computed in the previous step. The script provides a variety of options for the user to customize the evaluation process, including the choice of performance metrics and the choice of evaluation datasets.

A full listing of the options available for the viprs_evaluate script can be found by running the following command in your terminal:

viprs_evaluate -h

Which outputs the following help message:

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        Variational Inference of Polygenic Risk Scores
        Version: 0.1.0 | Release date: April 2024
        Author: Shadi Zabad, McGill University
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        < Evaluate the Prediction Accuracy of PRS >

usage: viprs_evaluate [-h] --prs-file PRS_FILE --phenotype-file PHENO_FILE [--phenotype-col PHENO_COL] [--phenotype-likelihood {gaussian,infer,binomial}]
                      --output-file OUTPUT_FILE [--metrics METRICS [METRICS ...]] [--covariates-file COVARIATES_FILE]

Commandline arguments for evaluating polygenic score estimates

optional arguments:
  -h, --help            show this help message and exit
  --prs-file PRS_FILE   The path to the PRS file (expected format: FID IID PRS, tab-separated)
  --phenotype-file PHENO_FILE
                        The path to the phenotype file. The expected format is: FID IID phenotype (no header), tab-separated.
  --phenotype-col PHENO_COL
                        The column index for the phenotype in the phenotype file (0-based index).
  --phenotype-likelihood {gaussian,infer,binomial}
                        The phenotype likelihood ("gaussian" for continuous, "binomial" for case-control). If not set, will be inferred automatically based on the
                        phenotype file.
  --output-file OUTPUT_FILE
                        The output file where to store the evaluation metrics (with no extension).
  --metrics METRICS [METRICS ...]
                        The evaluation metrics to compute (default: all available metrics that are relevant for the phenotype). For a full list of supported
                        metrics, check the documentation.
  --covariates-file COVARIATES_FILE
                        A file with covariates for the samples included in the analysis. This tab-separated file should not have a header and the first two columns
                        should be the FID and IID of the samples.