An integrated toolset for the analysis of de novo (sporadic) genetic sequence variants. denovolyzeR implements a mutational model that estimates the probability of a de novo genetic variant arising in each human gene, from which one can infer the expected number of de novo variants in a given population size. Observed variant frequencies can then be compared against expectation in a Poisson framework. denovolyzeR provides a suite of functions to implement these analyses for the interpretation of de novo variation in human disease.
denovolyzeByGenes()returned incorrect output if user overrode default variant classes analysed (using
includeClassesargument; column labels did not match data content)
new functionality includes analysis of sub-types of missense variation
argument names and output formats are about to change: this development release serves to preserce a working version of the package using first draft argument names
core statistical functionality is complete and ready for beta-testing
main limitation is a lack of error-catching
there may also be very minor modifications to underlying probability tables