Genotype classifiers
A genotype classifier assigns an individual into a class based on their genotype. In GPSEA, genotype classifiers leverage information from one of the three areas:
Sex
Disease diagnosis
Presence of variant(s) that meet certain inclusion criteria (e.g. a missense variant in heterozygous genotype)
Classification based on sex or disease diagnosis is relatively straightforward - the individuals are assigned by the biological sex or presence of a specific diagnosis. See Group by sex and Group by diagnosis for more details.
Partitioning based on variants is, however, much more flexible, to support the analysis of the broad spectrum of pathomechanisms that have been shown to lead to genetic diseases. In general, we first create one or more variant predicates to select the variants of interest (Variant Predicates), then count and interpret the number of alleles in the cohort members, including factors such as the expected mode of inheritance and sex, to assign the tested individual into a genotype group (Group by variant category or Group by allele count).