{"action":"created","issue":{"url":"https://api.github.com/repos/ISA-tools/stato/issues/63","repository_url":"https://api.github.com/repos/ISA-tools/stato","labels_url":"https://api.github.com/repos/ISA-tools/stato/issues/63/labels{/name}","comments_url":"https://api.github.com/repos/ISA-tools/stato/issues/63/comments","events_url":"https://api.github.com/repos/ISA-tools/stato/issues/63/events","html_url":"https://github.com/ISA-tools/stato/issues/63","id":295811654,"number":63,"title":"Best linear unbiased predictor definition in Stato","user":{"login":"bauchetg","id":12039071,"avatar_url":"https://avatars0.githubusercontent.com/u/12039071?v=4","gravatar_id":"","url":"https://api.github.com/users/bauchetg","html_url":"https://github.com/bauchetg","followers_url":"https://api.github.com/users/bauchetg/followers","following_url":"https://api.github.com/users/bauchetg/following{/other_user}","gists_url":"https://api.github.com/users/bauchetg/gists{/gist_id}","starred_url":"https://api.github.com/users/bauchetg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bauchetg/subscriptions","organizations_url":"https://api.github.com/users/bauchetg/orgs","repos_url":"https://api.github.com/users/bauchetg/repos","events_url":"https://api.github.com/users/bauchetg/events{/privacy}","received_events_url":"https://api.github.com/users/bauchetg/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-02-09T09:50:17Z","updated_at":"2018-02-12T10:08:53Z","closed_at":null,"author_association":"NONE","body":"Hi Stato team,\r\n\r\nI wondered if there is a plan for including Best linear unbiased predictions in stato.\r\nThis type of predictors is widely used in genomic selection in different ways (BLUP, gBLUP, etc..)\r\nto estimate breeding values.\r\nThanks for your input!\r\nCheers\r\n\r\nGuillaume"},"comment":{"url":"https://api.github.com/repos/ISA-tools/stato/issues/comments/364878196","html_url":"https://github.com/ISA-tools/stato/issues/63#issuecomment-364878196","issue_url":"https://api.github.com/repos/ISA-tools/stato/issues/63","id":364878196,"user":{"login":"bauchetg","id":12039071,"avatar_url":"https://avatars0.githubusercontent.com/u/12039071?v=4","gravatar_id":"","url":"https://api.github.com/users/bauchetg","html_url":"https://github.com/bauchetg","followers_url":"https://api.github.com/users/bauchetg/followers","following_url":"https://api.github.com/users/bauchetg/following{/other_user}","gists_url":"https://api.github.com/users/bauchetg/gists{/gist_id}","starred_url":"https://api.github.com/users/bauchetg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bauchetg/subscriptions","organizations_url":"https://api.github.com/users/bauchetg/orgs","repos_url":"https://api.github.com/users/bauchetg/repos","events_url":"https://api.github.com/users/bauchetg/events{/privacy}","received_events_url":"https://api.github.com/users/bauchetg/received_events","type":"User","site_admin":false},"created_at":"2018-02-12T10:08:53Z","updated_at":"2018-02-12T10:08:53Z","author_association":"NONE","body":"Hi Philippe,\r\n\r\nThank you for taking my request into account. \r\nIn a mixed linear model general definition like: y = XB + Zu + e\r\n\"B\" et \"u\" are the vector of fixed and random effect respectively, \"X\" and \"Z\" are the associated design matrices and \"e\" is a random residual vector. Random effect are assumed to be normally distributed and a variance covariance matrix V. Fixed effect being estimated by BLUE and random effects predicted through BLUP usually through restricted maximum likelihood (REML).\r\n\r\nIn plant breeding, for a standard trial phenotypic data analysis, the genotype effect is used as fixed (BLUE) or random (BLUP) in combination with other experimental factors (i.e. design). Genotypic value decomposition can be done trough additive or additive + non-additive (dominance + epistasis).\r\n-> These are the classic BLUP and BLUE ontological definition I would like to see in Stato.\r\n\r\nThe other BLUP definition of interest for Stato are in relation with genomic selection models.\r\nGenomic selection aims to predict the breeding value (GEBV) of a genotype using genomic best linear unbiased prediction (gBLUP). In gBLUP, a genomic relationship matrix is used, estimated from genomic data. It defines covariance between individuals based on observed similarity in genomic data, (instead of pedigree).\r\n\r\nThere are multiple ways of calculating these predictors through different relationship matrices/variance components (additive, dominance, additive+dominance, etc...)\r\n\r\nOntology wise, I don't know how much of these methological aspect can be included (so many exist and new ones are constantly being released) but I could suggest a few of interest for our research group.\r\n\r\nHaving such ontological terms woudl be of great help for many breeding systems and databases\r\nThanks for your help,\r\n\r\nBest regards,\r\n\r\nGuillaume"}}
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