log P_r: Calculate marginal probability of observed genotypes under 'pathogenic region' model
Description
Marginal probability calculated exactly by integration.Usage
"log P_r"(y, G, min_ac = 1L, q_shape = c(2, 4), p_shape = c(1, 1))
Arguments
y
Logical vector of case (TRUE) control (FALSE) status.
G
Integer/logical vector of genotypes by individual corresponding to case-control label y giving the 'rare variant counts'/'presence of rare variant indicators'.
min_ac
Minimum allele count per individual to be considered to have a pathogenic combination of variants. '1' could correspond to a dominant inheritance hypothesis whereas '2' could correspond to a recessive inheritance hypothesis.
q_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 min_ac variants.
p_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 min_ac variants.