gwasfilter: an R script to filter genome-wide association study

VernacularTitle:gwasfilter：用于筛选全基因组关联研究的R脚本
Author: Songchun YANG ¹ ; Chongyang LI ; Yizhen HU ; Qiufen SUN ; Jianqiao PAN ; Dianjianyi SUN ; Baoshan MA ; Jun LYU ; Liming LI
Author Information

1. 北京大学公共卫生学院流行病与卫生统计学系　100191
Keywords: Genome-wide association study; GWAS Catalog; R script
From: Chinese Journal of Epidemiology 2021;42(10):1876-1881
CountryChina
Language:Chinese
Abstract: Objective:To develop an R script that can efficiently and accurately filter genome-wide association studies (GWASs) from the GWAS Catalog Website.Methods:The selection principles of GWASs were established based on previous studies. The process of manual filtering in the GWAS Catalog was abstracted as standard algorithms. The R script (gwasfilter.R) was written by two programmers and tested many times.Results:It takes six steps for gwasfilter.R to filter GWASs. There are five main self-defined functions among this R script. GWASs can be filtered based on "whether the GWAS has been replicated" "sample size" "ethnicity of the study population" and other conditions. It takes no more than 1 second for this script to filter GWASs of a single trait.Conclusions:This R script (gwasfilter.R) is user-friendly and provides an efficient and standard process to filter GWASs flexibly. The source code is available at github ( https://github.com/lab319/gwas_filter).