region_association_evidence {BeviMed} | R Documentation |
Calculate evidence of under pathogenic locus model
Description
Marginal probability of model with aggregated allele counts.
Usage
region_association_evidence(y, G, min_ac = 1L, tau_shape = c(1, 1),
pi_shape = c(2, 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 |
Numeric vector of length the same as y or length 1 (in which case it is repeated to make it the same length as y ) giving the minimum number of alleles at pathogenic variant sites each individual requires in order to classify as having a ‘pathogenic allele configuration’. If For example, 1 could correspond to hypothesis of dominant inheritance hypothesis. If there are differences in ploidy between individuals in the locus, it is necessary to set it on an sample level basis - e.g. to incorporate information about gender if the locus lies on the X chromosome.
|
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 min_ac variants.
|
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 min_ac variants.
|
Value
Log marginal likelihood.
See Also
gamma0_evidence
[Package
BeviMed version 5.3
Index]