| 杨淞淳,李重阳,胡一祯,孙秋芬,潘建桥,孙点剑一,马宝山,吕筠,李立明.gwasfilter：用于筛选全基因组关联研究的R脚本[J].Chinese journal of Epidemiology,2021,42(10):1876-1881 |
| gwasfilter：用于筛选全基因组关联研究的R脚本 |
| gwasfilter: an R script to filter genome-wide association study |
| Received:July 31, 2020 |
| DOI：10.3760/cma.j.cn112338-20200731-01003 |
| KeyWord: 全基因组关联研究 GWAS Catalog R脚本 |
| English Key Word: Genome-wide association study GWAS Catalog R script |
| FundProject:国家自然科学基金（91846303，61471078） |
| Author Name | Affiliation | E-mail | | Yang Songchun | Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China | | | Li Chongyang | College of Information Science and Technology, Dalian Maritime University, Dalian 116026, China | | | Hu Yizhen | Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China | | | Sun Qiufen | Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China | | | Pan Jianqiao | College of Information Science and Technology, Dalian Maritime University, Dalian 116026, China | | | Sun Dianjianyi | Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China | | | Ma Baoshan | College of Information Science and Technology, Dalian Maritime University, Dalian 116026, China | mabaoshan@dlmu.edu.cn | | Lyu Jun | Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing 100191, China | lvjun@bjmu.edu.cn | | Li Liming | Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing 100191, China | |
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| Abstract: |
| 目的 开发一套能高效准确地从GWAS Catalog公开数据库中筛选全基因组关联研究（GWAS）的R脚本。方法 参考既往研究制定GWAS的筛选原则。将人工在GWAS Catalog的筛选过程抽象为标准的算法，2名程序员共同撰写R脚本（gwasfilter.R）后，由他人多次对脚本进行测试。结果 采用gwasfilter.R筛选GWAS包含6个步骤。该脚本内置5个主要函数，可以同时根据“是否有验证人群”“样本量大小”和“研究人群种族”等条件对GWAS进行筛选。筛选单个性状时，程序用时不超过1秒。结论 gwasfilter.R操作简便，筛选过程高效而标准化，可灵活应用于GWAS筛选。脚本源代码网址：https：//github.com/lab319/gwas_filter。 |
| English 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). |
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