lower_bound_gamma1_evidence {BeviMed} | R Documentation |
Calculate log lower bound for marginal probability of data under model gamma = 1 by summing likelihood over pathogenic variant partitions.
lower_bound_gamma1_evidence(y, G, min_ac = 1L, by_term = FALSE, tau_shape = c(1, 1), pi_shape = c(6, 1), omega_shape = c(2, 8), sum_over_variants = seq(length.out = ncol(G)))
y |
Logical vector of case ( |
G |
Integer matrix of variant counts per individual, one row per individual and one column per variant. |
min_ac |
Numeric vector of length the same as |
by_term |
Calculate probability that individual terms are pathogenic conditional on model gamma=1. |
tau_shape |
Beta shape hyper-priors for prior on rate of affection (i.e. being a case) amongst individuals with non-pathogenic variant combinations (i.e. they have less than |
pi_shape |
Beta shape hyper-priors for prior on rate of affection (i.e. being a case) amongst individuals with pathogenic variant combinations (i.e. they have at least |
omega_shape |
Beta shape hyper-priors for prior on rate of pathogenicity amongst variants. |
sum_over_variants |
Subset of variants for whose power set to calculate the direct sum over. |
Log of marginal likelihood.