{"action":"created","issue":{"url":"https://api.github.com/repos/lgatto/MSnbase/issues/114","repository_url":"https://api.github.com/repos/lgatto/MSnbase","labels_url":"https://api.github.com/repos/lgatto/MSnbase/issues/114/labels{/name}","comments_url":"https://api.github.com/repos/lgatto/MSnbase/issues/114/comments","events_url":"https://api.github.com/repos/lgatto/MSnbase/issues/114/events","html_url":"https://github.com/lgatto/MSnbase/issues/114","id":163519482,"number":114,"title":"Applying filtering and processing to different MS levels","user":{"login":"lgatto","id":384198,"avatar_url":"https://avatars.githubusercontent.com/u/384198?v=3","gravatar_id":"","url":"https://api.github.com/users/lgatto","html_url":"https://github.com/lgatto","followers_url":"https://api.github.com/users/lgatto/followers","following_url":"https://api.github.com/users/lgatto/following{/other_user}","gists_url":"https://api.github.com/users/lgatto/gists{/gist_id}","starred_url":"https://api.github.com/users/lgatto/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lgatto/subscriptions","organizations_url":"https://api.github.com/users/lgatto/orgs","repos_url":"https://api.github.com/users/lgatto/repos","events_url":"https://api.github.com/users/lgatto/events{/privacy}","received_events_url":"https://api.github.com/users/lgatto/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/lgatto/MSnbase/labels/MSnbase2","name":"MSnbase2","color":"bfdadc"}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":11,"created_at":"2016-07-02T13:54:16Z","updated_at":"2016-07-07T14:46:11Z","closed_at":null,"body":"Filtering (at least some) and processing function will need to be applied to different levels separately, with different parameters. \r\n* [ ] `filterMz`, which exists as `trimMz` (to be deprecated in favour of the former) - *lazy*\r\n* [ ] `removePeaks`, `clean` - *lazy*\r\n* [ ] `bin` - *lazy*\r\n* [ ] `pickPeaks` - *lazy*\r\n* [ ] `smooth` - *lazy*\r\n\r\nFor methods, the MS level is implicit\r\n* [ ] `quantify`: current methods only for MS2. Here, we can figure out based on the specific `method` - produces an `MSnSet` object.\r\n* [ ] `removePrecMz`, only relevant for MS2 - *lazy*\r\n* [ ] `removeReporters` only relevant for MS2 - *lazy*\r\n\r\nThese methods probably won't need it\r\n* [x] `filterRt` - *immediate*\r\n* [X] `filterMsLevel` - *immediate*\r\n* [x] `filterFile` - *immediate* (see #122)\r\n* [X] `filterAcquisitionNum` - immediate\r\n* [ ] `normalise`/`normalize` - *lazy*\r\n\r\n(See [here](https://github.com/lgatto/MSnbase/issues/106#issuecomment-229920000) for a definition of *lazy* and *immediate*)\r\n"},"comment":{"url":"https://api.github.com/repos/lgatto/MSnbase/issues/comments/231099923","html_url":"https://github.com/lgatto/MSnbase/issues/114#issuecomment-231099923","issue_url":"https://api.github.com/repos/lgatto/MSnbase/issues/114","id":231099923,"user":{"login":"jotsetung","id":5506112,"avatar_url":"https://avatars.githubusercontent.com/u/5506112?v=3","gravatar_id":"","url":"https://api.github.com/users/jotsetung","html_url":"https://github.com/jotsetung","followers_url":"https://api.github.com/users/jotsetung/followers","following_url":"https://api.github.com/users/jotsetung/following{/other_user}","gists_url":"https://api.github.com/users/jotsetung/gists{/gist_id}","starred_url":"https://api.github.com/users/jotsetung/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jotsetung/subscriptions","organizations_url":"https://api.github.com/users/jotsetung/orgs","repos_url":"https://api.github.com/users/jotsetung/repos","events_url":"https://api.github.com/users/jotsetung/events{/privacy}","received_events_url":"https://api.github.com/users/jotsetung/received_events","type":"User","site_admin":false},"created_at":"2016-07-07T14:46:11Z","updated_at":"2016-07-07T14:46:11Z","body":"Done with `normalize`(commit https://github.com/lgatto/MSnbase/commit/1c4e53766330c13394ca16b54c4f11f969f1f038).\r\nNext to the `msLevel` aware filters... I have to think a little bit how I'm going to do that for the *lazy* filters."}}
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