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Yang SC, Li CY, Hu YZ, Sun QF, Pan JQ, Sun DJY, Ma BS, Lyu J, Li LM. [gwasfilter: an R script to filter genome-wide association study]. Zhonghua Liu Xing Bing Xue Za Zhi 2021; 42:1876-1881. [PMID: 34814627 DOI: 10.3760/cma.j.cn112338-20200731-01003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
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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Affiliation(s)
- S C Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - C Y Li
- College of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Y Z Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Q F Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - J Q Pan
- College of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - D J Y Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - B S Ma
- College of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - J Lyu
- 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
| | - L M Li
- 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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Ma BS, Chang Q, Geng Y, Liu GH, Dong H, Sun YQ. 02 Brain cancer prediction using machine learning methods and high-throughput molecular data. J Investig Med 2017. [DOI: 10.1136/jim-2017-mebabstracts.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Affiliation(s)
- F. H. Su
- National Laboratory for Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083, China
| | - Z. L. Fang
- National Laboratory for Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083, China
| | - B. S. Ma
- National Laboratory for Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083, China
| | - K. Ding
- National Laboratory for Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083, China
| | - G. H. Li
- National Laboratory for Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083, China
| | - W. Chen
- Nomadics, Inc., 1024 South Innovation Way, Stillwater, Oklahoma 74074
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Ma BS, Li NM, Wang GR. [Clinical and experimental study of the effect of compound five-shen herbal drink in the treatment of acute febrile diseases with damage to the yin and reddened tongue syndrome]. Zhong Xi Yi Jie He Za Zhi 1989; 9:583-6, 579. [PMID: 2691106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Based on the experience of the late Beijing traditional medicine professor Zhao Bingnan in treating acute infectious febrile disease and its complications, compound herbal drink composed of five kinds of shen. Six hundred cases of febrile disease with damage to Yin and reddened tongue syndrome and hypokalemia. Patients were randomly divided into groups I, II and control. The perspective study of treatment results and experiments were carried out. The results showed that group I and II who received the compound five-Shen herbal drink (CFSHD) showed good therapeutic effects, the rates of significant effectiveness were 65.5% and 73.1% respectively (P greater than 0.05). The total rates of effectiveness were 97.2% and 96.2% respectively. The rate of significant effectiveness of the control group was 11%, total rate of effectiveness was 43%. There was significant statistical difference between the control group and group I or II (P less than 0.001). Authors of present paper are the first to propose the "Reddened Tongue" to be the main diagnostic criterion of syndrome of "Damage both to the Qi and Yin". Laboratory examination of 344 cases of "Reddened Tongue" revealed that 317 cases with hypokalemia (blood potassium less than 3.5 mEq/L) were 92.15% of the entire group. The authors point out that most of the patients with "damage to both the Qi and Yin" besides hypokalemia can be also low in calcium, magnesium and trace elements. After treatment with CFSHD restoration of normal blood potassium was parallel with the improvement of the reddened tongue.(ABSTRACT TRUNCATED AT 250 WORDS)
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Ma BS, Pei DK. [The application of wei chang fu yuan tang for the postoperation of abdomen--an observation on its clinical effects and experimental study]. Zhong Xi Yi Jie He Za Zhi 1986; 6:139-42, 130. [PMID: 2942295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Ma BS. [Preparation of Chinese traditional drugs in small pieces]. Zhong Yao Tong Bao 1983; 8:41-5. [PMID: 6228337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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