Predicates

Searching for genotype-phenotype associations usually requires that the individuals are partitioned into two or more discrete groups to allow testing for the inter-group differences. GPSEA reflects these requirements with its predicate API.

A predicate must be capable of partitioning the individuals into two or more groups. The groups must be exclusive - each individual must be assigned at most into one group. In general, it is desirable that the groups cover all or at least the majority of the cohort being analyzed to maximize statistical power. However, the predicate is allowed to return None if the individual cannot be assigned. As a result, the individual will be omitted from the downstream analysis.

Predicates serve both the genotype and phenotype prongs of the analysis. Genotype predicates (GenotypePolyPredicate) assign the Patient into a group (mostly) based on the variant information, while the phenotype predicates (PhenotypePolyPredicate) use the HPO terms to assign a group.

All GPSEA analyses need at least one predicate (typically a genotype predicate) and many require both genotype and phenotype predicates. The following pages provide more information.

Contents:

• Phenotype Predicates
• Genotype Predicates

Gallery

Here we show examples of predicates used in some of our analyses.

TODO

Need more?

Please see VariantPredicates and ProteinPredicates for a list of the predicates available off the shelf.

However, feel free to open an issue on our GitHub tracker if a predicate seems to be missing.