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Since we're now using the random forest to select latent variables for further analysis, I'd like to determine what our threshold is. Currently we've selected the 'top 10' by importance for each tumor type, and I've done some sort of hack to take the mean importances scores and get the top 10 of those.\r\n\r\nIs there some way to get the minimum variables needed to predict? It can be more than 10... But I'd like to use a concrete metric to base our downstream analysis, which includes:\r\n1- correlation with immune (20)\r\n2- correlation with MetaViper\r\n3- search for gene variants that predict LV differences\r\n4- interrogation of recount2data\r\n\r\nIs there some standard 'importance' threshold that we can use? Any other ideas? "},"comment":{"url":"https://api.github.com/repos/Sage-Bionetworks/NF_LandscapePaper_2019/issues/comments/558792988","html_url":"https://github.com/Sage-Bionetworks/NF_LandscapePaper_2019/issues/68#issuecomment-558792988","issue_url":"https://api.github.com/repos/Sage-Bionetworks/NF_LandscapePaper_2019/issues/68","id":558792988,"node_id":"MDEyOklzc3VlQ29tbWVudDU1ODc5Mjk4OA==","user":{"login":"sgosline","id":1847866,"node_id":"MDQ6VXNlcjE4NDc4NjY=","avatar_url":"https://avatars0.githubusercontent.com/u/1847866?v=4","gravatar_id":"","url":"https://api.github.com/users/sgosline","html_url":"https://github.com/sgosline","followers_url":"https://api.github.com/users/sgosline/followers","following_url":"https://api.github.com/users/sgosline/following{/other_user}","gists_url":"https://api.github.com/users/sgosline/gists{/gist_id}","starred_url":"https://api.github.com/users/sgosline/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sgosline/subscriptions","organizations_url":"https://api.github.com/users/sgosline/orgs","repos_url":"https://api.github.com/users/sgosline/repos","events_url":"https://api.github.com/users/sgosline/events{/privacy}","received_events_url":"https://api.github.com/users/sgosline/received_events","type":"User","site_admin":false},"created_at":"2019-11-26T19:56:21Z","updated_at":"2019-11-26T19:56:21Z","author_association":"COLLABORATOR","body":"Awesome, does this change the top40 lists at all? Also, can you please update syn21315356 to indicate, for each LV, which disease it was important to predict - something like this\r\n\r\n|LV | All| cNF | pNF|MPNST|NF|\r\n|---|---|---|---|---|---|\r\n|lv1|x|||x||\r\n"}}
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