avallonking/LRTq: Rare variant association test for quantitative traits with likelihood ratio test

LRTq, a powerful statistical method that infers causal statuses of rare variants with prior information and observational data and then aggregate rare variants in a nonlinear manner. With the assumption that individuals with abnormal gene expression levels are likely to enrich for causal rare variants, LRTq performs a likelihood ratio test to identify whether there are at least one causal rare variants in a group of variants near a gene. It first computes the ratio between the null model that assumes no causal rare variants in a variant set and the alternative model that asserts at least one causal rare variants. LRTq then calculates p-value for the likelihood ratio between these two models using permutation test.

install.packages("remotes")
remotes::install_github("avallonking/LRTq")