RVFam-package: Rare Variants Association Analyses with Family Data
In RVFam: Rare Variants Association Analyses with Family Data

RVFam package provides functions to perform single SNP association analyses and gene-based tests for continuos, binary and survival traits against sequencing variant genotypes (e.g. exome chip and whole genome sequencing data) using family data. The gene-based tests include two burden tests, most powerful when effects are in the same direction across all included variants (Li and Leal 2008 and Madsen and Browning 2009), and one directional insensitive test (Wei 2009). For single SNP association analyses of continuous traits, RVFam fits linear mixed effects (LME) model with relationship coefficcient matrix as within pedigree correlation matrix to account for familial correlation; for binary traits, RVFam fits generalized linear mixed effects (GLMM) model that treats each pedigree as a cluster; while for survival traits, RVFam fits Cox proportional hazards regression model (COXPH) with frailty that adds a random effect for family clusters.