Struglab/RVS: Robust Variance Score (RVS) test for association of variants from next generation sequence data with binary traits using external controls

Robust variance score test can be used for association when external sequencing control data is used. Its input is the variant call format (VCF) file from the next generation sequencing (NGS) data. Compared to the conventional score test, it used robust variance for the score statistic which used the conditional genotype probabilities calculated from the VCF file. For details about the RVS method, please see the paperpublished in bioinformatics, 2014: Derkach et al, Association analysis using next-generation sequence data from publicly available control groups: the robust variance score statistic. The package include four modules: simulate sequence data for given parameters (generate_seqdata); retrieve information form the vcf file (vcf_process); association test from the expected genotype probability (RVS_asy, RVS_btrap for common variants and RVS_rare for rare variants) and association test from genotype calls (regScore_Rao, regScore_btrap, regScore_rare).

install.packages("remotes")
remotes::install_github("Struglab/RVS")