{"action":"created","issue":{"url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1216","labels_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1216/labels{/name}","comments_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1216/comments","events_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1216/events","html_url":"https://github.com/OpenMS/OpenMS/issues/1216","id":55775092,"number":1216,"title":"IDs should be assigned to sub-features of a ConsensusFeature.","user":{"login":"lars20070","id":6149805,"avatar_url":"https://avatars.githubusercontent.com/u/6149805?v=3","gravatar_id":"","url":"https://api.github.com/users/lars20070","html_url":"https://github.com/lars20070","followers_url":"https://api.github.com/users/lars20070/followers","following_url":"https://api.github.com/users/lars20070/following{/other_user}","gists_url":"https://api.github.com/users/lars20070/gists{/gist_id}","starred_url":"https://api.github.com/users/lars20070/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lars20070/subscriptions","organizations_url":"https://api.github.com/users/lars20070/orgs","repos_url":"https://api.github.com/users/lars20070/repos","events_url":"https://api.github.com/users/lars20070/events{/privacy}","received_events_url":"https://api.github.com/users/lars20070/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-01-28T16:01:51Z","updated_at":"2015-01-29T11:06:49Z","closed_at":null,"body":"Currently, IDs are assigned to the entire ConsensusFeature, not the individual sub features. In the case of label-free data, it is no longer clear which map the ID came from. In the case of isotopically labelled data, it is no longer clear if the ID was mapped to the light or heavy partner.\r\n\r\nConsider a triple dimethylation experiment with the labels +28Da, +32Da and +36Da. The peptide feature detection identified many triplets [light, medium, heavy], but also a couple of doublets and singlets. Then IDs were mapped to these multiplets. Now the doublets and singlets need to be filled up with zero-intensity-peptide-features before being passed (now all of them triplets) to the ProteinQuantifier. If say a medium ID (+32Da) was mapped to the \"light\" partner of a +4Da doublet, the doublet needs to be extended to the left i.e. [0, \"light\", \"heavy\"]. If the medium ID was mapped to \"heavy\", the doublet needs to extended to the right i.e. [\"light\",\"heavy\", 0]. (This is the job of a small MultiplexResolver tool I am working on.)\r\n\r\nIs there a hack to assign IDs to the individual sub-features of a consensus using our existing data structure?"},"comment":{"url":"https://api.github.com/repos/OpenMS/OpenMS/issues/comments/72007333","html_url":"https://github.com/OpenMS/OpenMS/issues/1216#issuecomment-72007333","issue_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1216","id":72007333,"user":{"login":"hendrikweisser","id":2251068,"avatar_url":"https://avatars.githubusercontent.com/u/2251068?v=3","gravatar_id":"","url":"https://api.github.com/users/hendrikweisser","html_url":"https://github.com/hendrikweisser","followers_url":"https://api.github.com/users/hendrikweisser/followers","following_url":"https://api.github.com/users/hendrikweisser/following{/other_user}","gists_url":"https://api.github.com/users/hendrikweisser/gists{/gist_id}","starred_url":"https://api.github.com/users/hendrikweisser/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hendrikweisser/subscriptions","organizations_url":"https://api.github.com/users/hendrikweisser/orgs","repos_url":"https://api.github.com/users/hendrikweisser/repos","events_url":"https://api.github.com/users/hendrikweisser/events{/privacy}","received_events_url":"https://api.github.com/users/hendrikweisser/received_events","type":"User","site_admin":false},"created_at":"2015-01-29T11:06:49Z","updated_at":"2015-01-29T11:06:49Z","body":"@lars20070:\r\n> Now the doublets and singlets need to be filled up with zero-intensity-peptide-features before being passed (now all of them triplets) to the ProteinQuantifier.\r\n\r\nWhy is that necessary? If there are missing features in some sub-maps, isn't the missing value already represented as zero?"}}