region_association_evidence: Calculate evidence of under pathogenic locus model

Description Usage Arguments Value See Also

View source: R/functions.R

Description

Marginal probability of model with aggregated allele counts.

Usage

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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


BeviMed documentation built on Aug. 21, 2017, 5:05 p.m.