which "project" object you mean here?

[Dahn-YoungDong]

LanGen_pipeline_version2/1.1_FILTERING_SNPs.R

Lines 893 to 908 in d98a65e

	###7.3. FST OUTLIER DETECTION
	#A. Compute results for the best run
	res = Gettess3res(tess3.ls, K=optimal_K)
	#B. Select FST statistics for the best run
	FST = res$Fst
	#C. Compute the GIF - genomic inflation factor
	lambda = res$gif
	lambda # 3.750238
	#D. Compute adjusted p-values from the combined z-scores and plot histogram of p-values
	n = dim(Q(project, run, optimal_K))[1]
	z.scores = sqrt(FST*(n-optimal_K)/(1-FST))
	adj.p.values = pchisq(z.scores^2/lambda, df = optimal_K-1, lower = FALSE)
	hist(adj.p.values, col = "red")

Hello Jeronymo,

I am at this chunk of code, using tess3 method to do spatial genetic structuring.

at the line 905, which "project" object do you mean? Maybe you mean the best run object called "res" at line 895?

Thanks,

[jdalapicolla]

Hi Dahn-Young I'm sorry for didn't you reply to you before but I'm teaching some classes and I don't have time to answer you properly: 1) If you need only to map the variation for your discipline, you don't need R to do this. I use QGIS to create maps for publications. This script is only for visualization. For Qgis there's a lot of tutorials on Youtube. 2) On "project", yep, it is the best-run of res that you selected. Thanks for showing me this error I will fix it when I have time. Best, *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 dom., 29 de nov. de 2020 às 23:19, Dahn-Young Dong < [email protected]> escreveu:

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https://github.com/jdalapicolla/LanGen_pipeline_version2/blob/d98a65e128e810a39b516a9dac40eaae48b856de/1.1_FILTERING_SNPs.R#L893-L908 Hello Jeronymo, I am at this chunk of code, using tess3 method to do spatial genetic structuring. at the line 905, which "project" object do you mean? Maybe you mean the best run object called "res" at line 895? Thanks, — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIGPCMF56XBLIMTGX5OE3PLSSL6M3ANCNFSM4UG6KCSQ> .