This is a method for Allele-specific DNA Copy Number profiling for whole-Exome sequencing data.  Given the allele-specific coverage and site biases at the variant loci, this program segments the genome into regions of homogeneous allele-specific copy number.  It requires, as input, the read counts for each variant allele in a pair of case and control samples, as well as the site biases. For detection of somatic mutations, the case and control samples can be the tumor and normal sample from the same individual.  The implemented method is based on the paper: Chen, H., Jiang, Y., Maxwell, K., Nathanson, K. and Zhang, N. (under review). Allele-specific copy number estimation by whole Exome sequencing.

Given vectors of family sizes and number of affecteds per family, calculates the risk of disease recurrence in an unaffected person, conditional on a family having at least k affected members. Methods also model heterogeneity of disease risk across families by fitting a mixture model, allowing for high and low risk families.

Fatty acid metabolic analysis aimed to the estimation of FA import (I), de novo synthesis (S), fractional contribution of the 13C-tracers (D0, D1, D2), elongation (E) and desaturation (Des) based on mass isotopologue data.

Simulates age-at-onset traits associated with a segregating major gene in family data 
     obtained from population-based, clinic-based, or multi-stage designs. Appropriate ascertainment 
     correction is utilized to estimate age-dependent penetrance functions either parametrically from 
     the fitted model or nonparametrically from the data. The Expectation and Maximization algorithm 
     can infer missing genotypes and carrier probabilities estimated from family's genotype and
     phenotype information or from fitted models. Plot functions include pedigrees of simulated 
     families and predicted penetrance curves based on specified parameter values.
     For more information see Choi, Y.-H., Briollais, L., He, W. and Kopciuk, K. (2021) FamEvent: An 
     R Package for Generating and Modeling Time-to-Event Data in Family Designs, 
     Journal of Statistical Software 97 (7), 1-30.