{"action":"created","issue":{"url":"https://api.github.com/repos/Bioconductor/Contributions/issues/50","repository_url":"https://api.github.com/repos/Bioconductor/Contributions","labels_url":"https://api.github.com/repos/Bioconductor/Contributions/issues/50/labels{/name}","comments_url":"https://api.github.com/repos/Bioconductor/Contributions/issues/50/comments","events_url":"https://api.github.com/repos/Bioconductor/Contributions/issues/50/events","html_url":"https://github.com/Bioconductor/Contributions/issues/50","id":164128360,"number":50,"title":"GAprediction","user":{"login":"JonBohlin","id":20295285,"avatar_url":"https://avatars.githubusercontent.com/u/20295285?v=3","gravatar_id":"","url":"https://api.github.com/users/JonBohlin","html_url":"https://github.com/JonBohlin","followers_url":"https://api.github.com/users/JonBohlin/followers","following_url":"https://api.github.com/users/JonBohlin/following{/other_user}","gists_url":"https://api.github.com/users/JonBohlin/gists{/gist_id}","starred_url":"https://api.github.com/users/JonBohlin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JonBohlin/subscriptions","organizations_url":"https://api.github.com/users/JonBohlin/orgs","repos_url":"https://api.github.com/users/JonBohlin/repos","events_url":"https://api.github.com/users/JonBohlin/events{/privacy}","received_events_url":"https://api.github.com/users/JonBohlin/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/Bioconductor/Contributions/labels/2.%20review%20in%20progress","name":"2. review in progress","color":"1881c2"},{"url":"https://api.github.com/repos/Bioconductor/Contributions/labels/OK","name":"OK","color":"228822"}],"state":"open","locked":false,"assignee":{"login":"mtmorgan","id":118552,"avatar_url":"https://avatars.githubusercontent.com/u/118552?v=3","gravatar_id":"","url":"https://api.github.com/users/mtmorgan","html_url":"https://github.com/mtmorgan","followers_url":"https://api.github.com/users/mtmorgan/followers","following_url":"https://api.github.com/users/mtmorgan/following{/other_user}","gists_url":"https://api.github.com/users/mtmorgan/gists{/gist_id}","starred_url":"https://api.github.com/users/mtmorgan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mtmorgan/subscriptions","organizations_url":"https://api.github.com/users/mtmorgan/orgs","repos_url":"https://api.github.com/users/mtmorgan/repos","events_url":"https://api.github.com/users/mtmorgan/events{/privacy}","received_events_url":"https://api.github.com/users/mtmorgan/received_events","type":"User","site_admin":false},"assignees":[{"login":"mtmorgan","id":118552,"avatar_url":"https://avatars.githubusercontent.com/u/118552?v=3","gravatar_id":"","url":"https://api.github.com/users/mtmorgan","html_url":"https://github.com/mtmorgan","followers_url":"https://api.github.com/users/mtmorgan/followers","following_url":"https://api.github.com/users/mtmorgan/following{/other_user}","gists_url":"https://api.github.com/users/mtmorgan/gists{/gist_id}","starred_url":"https://api.github.com/users/mtmorgan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mtmorgan/subscriptions","organizations_url":"https://api.github.com/users/mtmorgan/orgs","repos_url":"https://api.github.com/users/mtmorgan/repos","events_url":"https://api.github.com/users/mtmorgan/events{/privacy}","received_events_url":"https://api.github.com/users/mtmorgan/received_events","type":"User","site_admin":false}],"milestone":null,"comments":30,"created_at":"2016-07-06T17:17:15Z","updated_at":"2016-07-25T13:21:48Z","closed_at":null,"body":"Update the following URL to point to the GitHub repository of\r\nthe package you wish to submit to _Bioconductor_\r\n\r\n- Repository: https://github.com/JonBohlin/GAprediction\r\n\r\nConfirm the following by editing each check box to '[x]'\r\n\r\n- [X] I understand that by submitting my package to _Bioconductor_,\r\n  the package source and all review commentary are visible to the\r\n  general public.\r\n\r\n- [X] I have read the _Bioconductor_ [Package Submission][2]\r\n  instructions. My package is consistent with the _Bioconductor_\r\n  [Package Guidelines][1].\r\n\r\n- [X] My package addresses statistical or bioinformatic issues related\r\n  to the analysis and comprehension of high throughput genomic data.\r\n\r\n- [X] I am committed to the long-term maintenance of my package. This\r\n  includes monitoring the [support site][3] for issues that users may\r\n  have, subscribing to the [bioc-devel][4] mailing list to stay aware\r\n  of developments in the _Bioconductor_ community, responding promptly\r\n  to requests for updates from the Core team in response to changes in\r\n  _R_ or underlying software.\r\n\r\nI am familiar with the essential aspects of _Bioconductor_ software\r\nmanagement, including:\r\n\r\n- [X] The 'devel' branch for new packages and features.\r\n- [X] The stable 'release' branch, made available every six\r\n      months, for bug fixes.\r\n- [X] _Bioconductor_ version control using [Subversion][5]\r\n  (optionally [via GitHub][6]).\r\n\r\nFor help with submitting your package, please subscribe and post questions\r\nto the [bioc-devel][4] mailing list.\r\n\r\n[1]: https://bioconductor.org/developers/package-guidelines/\r\n[2]: https://bioconductor.org/developers/package-submission/\r\n[3]: https://support.bioconductor.org\r\n[4]: https://stat.ethz.ch/mailman/listinfo/bioc-devel\r\n[5]: http://bioconductor.org/developers/how-to/source-control/\r\n[6]: http://bioconductor.org/developers/how-to/git-mirrors/\r\n"},"comment":{"url":"https://api.github.com/repos/Bioconductor/Contributions/issues/comments/234951040","html_url":"https://github.com/Bioconductor/Contributions/issues/50#issuecomment-234951040","issue_url":"https://api.github.com/repos/Bioconductor/Contributions/issues/50","id":234951040,"user":{"login":"JonBohlin","id":20295285,"avatar_url":"https://avatars.githubusercontent.com/u/20295285?v=3","gravatar_id":"","url":"https://api.github.com/users/JonBohlin","html_url":"https://github.com/JonBohlin","followers_url":"https://api.github.com/users/JonBohlin/followers","following_url":"https://api.github.com/users/JonBohlin/following{/other_user}","gists_url":"https://api.github.com/users/JonBohlin/gists{/gist_id}","starred_url":"https://api.github.com/users/JonBohlin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JonBohlin/subscriptions","organizations_url":"https://api.github.com/users/JonBohlin/orgs","repos_url":"https://api.github.com/users/JonBohlin/repos","events_url":"https://api.github.com/users/JonBohlin/events{/privacy}","received_events_url":"https://api.github.com/users/JonBohlin/received_events","type":"User","site_admin":false},"created_at":"2016-07-25T13:21:48Z","updated_at":"2016-07-25T13:21:48Z","body":"Thank you very much for taking the time to review my code and for your excelent comments. I have included a point-to-point response to them below. Your comments start with a bulletpoint, my responses are in _italic_\r\n\r\n•\tSince the central function of the package processes HumanMethylation450k arrays, it seems like predictGA should accept the output of common upstream software for processing this data, e.g., minfi(??). Likely this can be accomplished by writing a one-line test / coercion inside predictGA that extracts the relevant matrix if the argument is of the appropriate type. Likely this also requires at least adding the relevant package where the class and accessor are defined to the Suggests: field of the DESCRIPTION file, or better Import:'ing the relevant package and functions.\r\n\r\n_Yes, this is a good idea. However, there are many different packages used for treating HumanMethylation450k data having myself used Minfi, WateRmellon and Methylumi. Unfortunately, there is no standard method (yet?) for extracting the beta-matrix which is required by the GA predictor. All the packages mentioned above are quite comprehensive and I’d like to keep this program as small and independent as possible._\r\n\r\n•\tA LICENSCE file is not needed for GPL-2; please remove it\r\n\r\n_Removed_\r\n\r\n•\tuse message() rather than cat() to communicate with the user; messages can be suppressed via suppressMessages()\r\n\r\n_OK, thanks!_\r\n\r\n•  include context in error messages, rather than printing the error\r\nmessage to the screen and stopping uninformatively, e.g., at\r\npredictGA.R:32 write\r\n  stop(\"Missing essential CpGs needed for prediction\\n\"\r\n        predictorSites[temp], \"\\n\")\r\n\r\n_OK_\r\n\r\n•  vectorize rather than iterate, for instance at predictGA.R:53\r\nfor(i in predictorSites)\r\n    predMatr[,i]<-mldat[,i]\r\nis I think just predMatr[, predictorSites] <- mldat[, predictorSites]\r\n\r\n_Thanks!_\r\n\r\n•\texplicitly invoking the garbage collector, e.g., at predictGA.R:68\r\nis seldom necessary; these objects will be available for garbage\r\ncollection as soon as the function ends, i.e., after the next line.\r\n\r\n_Thanks!_\r\n\r\n•\t It seems like the UL.mod.cv data is a central component of the model, and its derivation should be described explicitly (e.g., as a script in inst/script/.\r\n\r\n_An accompanying paper is under review and there everything is explained in detail. One of the reviewers wanted us to write a package to do GA prediction and so I did. Hopefully, the paper will be accepted soon._\r\n\r\n•\tconsider adding spaces around <- in the man pages; this makes the code more readable.\r\n\r\n_OK_\r\n"}}
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