{"action":"created","issue":{"url":"https://api.github.com/repos/GuangchuangYu/ChIPseeker/issues/43","repository_url":"https://api.github.com/repos/GuangchuangYu/ChIPseeker","labels_url":"https://api.github.com/repos/GuangchuangYu/ChIPseeker/issues/43/labels{/name}","comments_url":"https://api.github.com/repos/GuangchuangYu/ChIPseeker/issues/43/comments","events_url":"https://api.github.com/repos/GuangchuangYu/ChIPseeker/issues/43/events","html_url":"https://github.com/GuangchuangYu/ChIPseeker/issues/43","id":190801085,"number":43,"title":"Peak Annotations","user":{"login":"girdhar3","id":12140269,"avatar_url":"https://avatars.githubusercontent.com/u/12140269?v=3","gravatar_id":"","url":"https://api.github.com/users/girdhar3","html_url":"https://github.com/girdhar3","followers_url":"https://api.github.com/users/girdhar3/followers","following_url":"https://api.github.com/users/girdhar3/following{/other_user}","gists_url":"https://api.github.com/users/girdhar3/gists{/gist_id}","starred_url":"https://api.github.com/users/girdhar3/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/girdhar3/subscriptions","organizations_url":"https://api.github.com/users/girdhar3/orgs","repos_url":"https://api.github.com/users/girdhar3/repos","events_url":"https://api.github.com/users/girdhar3/events{/privacy}","received_events_url":"https://api.github.com/users/girdhar3/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-11-21T18:38:37Z","updated_at":"2016-11-22T04:50:03Z","closed_at":null,"body":"Hi \r\nI have a peak file p1. I annotate files\r\npeakAnno <- annotatePeak(p1,tssRegion=c(-3000, 3000),TxDb=txdb, annoDb=\"org.Hs.eg.db\")\r\nfeatures = attributes(peakAnno)\r\n\r\nI looked at head(features['detailGenomicAnnotation'][[1]])\r\nfor every peak it has multiple columns true. Why?\r\nI want to know exactly, how do you assign promoter region to a peak."},"comment":{"url":"https://api.github.com/repos/GuangchuangYu/ChIPseeker/issues/comments/262147048","html_url":"https://github.com/GuangchuangYu/ChIPseeker/issues/43#issuecomment-262147048","issue_url":"https://api.github.com/repos/GuangchuangYu/ChIPseeker/issues/43","id":262147048,"user":{"login":"girdhar3","id":12140269,"avatar_url":"https://avatars.githubusercontent.com/u/12140269?v=3","gravatar_id":"","url":"https://api.github.com/users/girdhar3","html_url":"https://github.com/girdhar3","followers_url":"https://api.github.com/users/girdhar3/followers","following_url":"https://api.github.com/users/girdhar3/following{/other_user}","gists_url":"https://api.github.com/users/girdhar3/gists{/gist_id}","starred_url":"https://api.github.com/users/girdhar3/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/girdhar3/subscriptions","organizations_url":"https://api.github.com/users/girdhar3/orgs","repos_url":"https://api.github.com/users/girdhar3/repos","events_url":"https://api.github.com/users/girdhar3/events{/privacy}","received_events_url":"https://api.github.com/users/girdhar3/received_events","type":"User","site_admin":false},"created_at":"2016-11-22T04:50:03Z","updated_at":"2016-11-22T04:50:03Z","body":"My question is when you get the TXDB object which has a list of annotated\nTSS.\n\nHow do you find the overlap of a peak with these regions? what is the min\nand maximum base pair overlap?\n\n\n\nKG\n\nOn Mon, Nov 21, 2016 at 8:41 PM, Guangchuang Yu <notifications@github.com>\nwrote:\n\n> If it was located within tssRegion=c(-3000, 3000), it will be assign to\n> promoter.\n>\n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub\n> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GuangchuangYu_ChIPseeker_issues_43-23issuecomment-2D262123031&d=DQMCaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=XW5NHlYxJyov09gidSvHlCx2roVNYW1IqPo7Rmin2pE&m=Mn05475yzKmMo9T0x8QnNjl3jzwNl7aC78RpzprrO5o&s=1QGgEHKF1TDCd8aoL0avNkiVRBlU6YYh1FNYik3tmGA&e=>,\n> or mute the thread\n> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ALk-2D7SwbdM8Wlss6XYXQ-2DWWKfOioU-2D3Kks5rAkgzgaJpZM4K4jBc&d=DQMCaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=XW5NHlYxJyov09gidSvHlCx2roVNYW1IqPo7Rmin2pE&m=Mn05475yzKmMo9T0x8QnNjl3jzwNl7aC78RpzprrO5o&s=nPkySgnpqqr8L3ohvuAhY4ApFIIKOnaJZ_8gMnDuFZg&e=>\n> .\n>\n"}}
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