cellregmap.run_interaction

cellregmap.run_interaction(y, E, G, W=None, E1=None, E2=None, hK=None, idx_G=None)[source]

Interaction test.

Test for cell-level genetic effects due to GxC interactions.

Compute p-values using a score test.

Parameters

  • y (array) – Phenotype

  • E (array) – Cellular contexts (GxC component)

  • G (array) – Genotypes (expanded)

  • W (array) – Fixed effect covariates

  • hK (array) – decompositon of kinship matrix (expanded)

  • E1 (array) – Cellular contexts (C component)

  • E2 (array) – Cellular contexts (K*C component)

  • idx_G (array) – Permuted genotype index

Returns

pvalues – P-values.

Return type

ndarray