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subset_variants
, which retains only variants with data bearing upon pathogenicity.omega
even when not explicitly sampled in summary.BeviMed_m
.bevimed_polytomous
function added which enables application of BeviMed across multiple association models.BeviMed
objects now more general, representing results of inference with respect to the baseline model gamma = 0
and an arbitrary number of alternative association models - typically, one for each mode of inheritance. The $moi
slot has been replaced with $models
.prob_pathogenic
now returns a list when broken down by mode of inheritance/model.bevimed
function now replaced by bevimed_m
, with the _m
indicating that it conditions on mode of inheritance.bevimed
now integrates over indicator of association (gamma) and mode of inheritance (m), allowing user to specify priors on probability of association and probability of dominance.BeviMed
class object has been replaced by BeviMed_m
, and a new BeviMed
class has been introduced for inference with respect to all models: gamma 0 and gamma 1 under each mode of inheritance.BeviMed Guide
which relates the package to the paper.print
ing a BeviMed
object now shows conditional probabilities of pathogenicity for each mode of inheritance, and expected explained cases and expected explaining variants shown too.bevimed
function to match the names of variables in the paper (under submission).G
should now be supplied as a matrix with rows corresponding to individuals, not variants.expected_explained
and explaining_variants
functions have been added, respectively computing the expected number of cases with their disease explained by the given variants, and expected number of pathogenic variants present amongst cases.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.