cellregmap.estimate_betas

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

Effect sizes estimator

Estimates cell-level genetic effects due to GxC as well as persistent genetic effects across all cells.

Parameters

  • y (array) – Phenotype

  • W (array) – Fixed effect covariates

  • E (array) – Cellular contexts

  • G (array) – Genotypes (expanded)

  • maf (array) – Minor allele frequencies (MAFs) for the SNPs in G

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

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

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

Returns

betas – estimated effect sizes, both persistent and due to GxC.

Return type

ndarray