{"action":"opened","issue":{"url":"https://api.github.com/repos/BushmanLab/geneTherapyPatientReportMaker/issues/23","labels_url":"https://api.github.com/repos/BushmanLab/geneTherapyPatientReportMaker/issues/23/labels{/name}","comments_url":"https://api.github.com/repos/BushmanLab/geneTherapyPatientReportMaker/issues/23/comments","events_url":"https://api.github.com/repos/BushmanLab/geneTherapyPatientReportMaker/issues/23/events","html_url":"https://github.com/BushmanLab/geneTherapyPatientReportMaker/issues/23","id":97050236,"number":23,"title":"Over calculating the number of actual unique sites.","user":{"login":"cnobles","id":12237291,"avatar_url":"https://avatars.githubusercontent.com/u/12237291?v=3","gravatar_id":"","url":"https://api.github.com/users/cnobles","html_url":"https://github.com/cnobles","followers_url":"https://api.github.com/users/cnobles/followers","following_url":"https://api.github.com/users/cnobles/following{/other_user}","gists_url":"https://api.github.com/users/cnobles/gists{/gist_id}","starred_url":"https://api.github.com/users/cnobles/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cnobles/subscriptions","organizations_url":"https://api.github.com/users/cnobles/orgs","repos_url":"https://api.github.com/users/cnobles/repos","events_url":"https://api.github.com/users/cnobles/events{/privacy}","received_events_url":"https://api.github.com/users/cnobles/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-07-24T13:14:11Z","updated_at":"2015-07-24T13:14:11Z","closed_at":null,"body":"For example:\r\n```\r\n                     |............in depth analysis........... |.......report.......|\r\n                      uniSites    multiSites     totalSites       uniSites\r\nGTSP0470       19455            536          19991         20528 \r\nGTSP0467         4908              39            4947           4982 \r\nGTSP0469         9720          1010          10730         10137 \r\nGTSP0471           953          1864            2817             969 \r\nGTSP0473           249              91              340             530 \r\nGTSP0472             56                9                65             155 \r\nGTSP0468           334            113              447             354 \r\n```\r\nThe number of unique sites should be calculated for each GTSP, and not from each replicate and then added together. This may be the case in what's going on, but one way we could solve this problem is by asking length(unique(sites[GTSP]$posID)) after all the replicates have been standardized together.\r\n\r\nOtherwise the issue may lie in the way we are standardizing sites, calling several sites near each other unique because the tail for the original site was > 5 nt. "}}