jdalapicolla
commented
3 years ago Hello,
R2 is the correlation limit for linkage disequilibrium. You can choose any value between 0 and 1, depending on the analyses you like to perform. 0 for filtering only independent SNPs and 1 for allowing SNPs completely linked.
Jeronymo Dalapicolla Biólogo | Biologist | CRBio 91.859/02-D Instituto Tecnológico Vale | Vale Institute of Technology Desenvolvimento Sustentável | Sustainable Development Rua Boaventura da Silva, 955 - Nazaré, Belém, Pará Phone: +55 (19) 998559340 Skype: @jeronymod CV Lattes http://lattes.cnpq.br/0831988373556961 GitHub https://github.com/jdalapicolla Google Scholar https://scholar.google.com.br/citations?user=09ArXn4AAAAJ&hl=en ORCID https://orcid.org/0000-0002-4819-9720 ResearchGate https://www.researchgate.net/profile/Jeronymo_Dalapicolla Publons http://www.researcherid.com/rid/D-4711-2016 AcademiaEdu https://independent.academia.edu/JeronymoDalapicolla LinkedIn https://www.linkedin.com/in/jeronymo-dalapicolla-3862b16b
Em sex., 4 de dez. de 2020 às 17:10, Dahn-Young Dong < notifications@github.com> escreveu:
Hello Jeronymo. Thank you for your previous help.
How did you determine this r2 value? I couldn't find it in the code. Can you share a resource or tutorial ?
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https://github.com/jdalapicolla/LanGen_pipeline_version2/blob/d98a65e128e810a39b516a9dac40eaae48b856de/1.1_FILTERING_SNPs.R#L316-L317
Hello Jeronymo. Thank you for your previous help.
How did you determine this r2 value? I couldn't find it in the code. Can you share a resource or tutorial ?