{"action":"created","issue":{"url":"https://api.github.com/repos/rmkoesterer/uga/issues/21","repository_url":"https://api.github.com/repos/rmkoesterer/uga","labels_url":"https://api.github.com/repos/rmkoesterer/uga/issues/21/labels{/name}","comments_url":"https://api.github.com/repos/rmkoesterer/uga/issues/21/comments","events_url":"https://api.github.com/repos/rmkoesterer/uga/issues/21/events","html_url":"https://github.com/rmkoesterer/uga/issues/21","id":177269715,"number":21,"title":"output single variant result in gene-based test","user":{"login":"shirley0818","id":21349340,"avatar_url":"https://avatars.githubusercontent.com/u/21349340?v=3","gravatar_id":"","url":"https://api.github.com/users/shirley0818","html_url":"https://github.com/shirley0818","followers_url":"https://api.github.com/users/shirley0818/followers","following_url":"https://api.github.com/users/shirley0818/following{/other_user}","gists_url":"https://api.github.com/users/shirley0818/gists{/gist_id}","starred_url":"https://api.github.com/users/shirley0818/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shirley0818/subscriptions","organizations_url":"https://api.github.com/users/shirley0818/orgs","repos_url":"https://api.github.com/users/shirley0818/repos","events_url":"https://api.github.com/users/shirley0818/events{/privacy}","received_events_url":"https://api.github.com/users/shirley0818/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2016-09-15T19:42:46Z","updated_at":"2016-09-16T18:47:54Z","closed_at":null,"body":"Using the gene-based pipeline \"uga snvgroup\", the output fine includes pvalue, pvalue_min, , cmac and nsnps. I am wondering whether the pipeline can output snp_id, cmac, pvalue, etc for each SNP included in the gene-based test for each gene. \r\n\r\nMany thanks,\r\nXiaoling "},"comment":{"url":"https://api.github.com/repos/rmkoesterer/uga/issues/comments/247677878","html_url":"https://github.com/rmkoesterer/uga/issues/21#issuecomment-247677878","issue_url":"https://api.github.com/repos/rmkoesterer/uga/issues/21","id":247677878,"user":{"login":"shirley0818","id":21349340,"avatar_url":"https://avatars.githubusercontent.com/u/21349340?v=3","gravatar_id":"","url":"https://api.github.com/users/shirley0818","html_url":"https://github.com/shirley0818","followers_url":"https://api.github.com/users/shirley0818/followers","following_url":"https://api.github.com/users/shirley0818/following{/other_user}","gists_url":"https://api.github.com/users/shirley0818/gists{/gist_id}","starred_url":"https://api.github.com/users/shirley0818/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shirley0818/subscriptions","organizations_url":"https://api.github.com/users/shirley0818/orgs","repos_url":"https://api.github.com/users/shirley0818/repos","events_url":"https://api.github.com/users/shirley0818/events{/privacy}","received_events_url":"https://api.github.com/users/shirley0818/received_events","type":"User","site_admin":false},"created_at":"2016-09-16T18:47:54Z","updated_at":"2016-09-16T18:47:54Z","body":"I will check the parameters first and then let you if I have further questions:)\n\nMany thanks and have a nice weekend,\nXiaoling\n---\n\nXiaoling Zhang, Ph.D.\nAssistant Professor of Medicine and Biostatistics\nSection of Biomedical Genetics\nBoston University School of Medicine\n72 East Concord Street, Room E223\nBoston, MA  02118-2526\nTel:  617-638-5040\nhttp://www.bumc.bu.edu/genetics\n________________________________\nFrom: Ryan Koesterer [notifications@github.com]\nSent: Friday, September 16, 2016 2:38 PM\nTo: rmkoesterer/uga\nCc: Zhang, Xiaoling; Author\nSubject: Re: [rmkoesterer/uga] output single variant result in gene-based test (#21)\n\n\nDo you know why it isn't being test? Is there a frequency threshold being used? You can set basically any of the parameters that are available in seqMeta. If you don't set them, then the defaults are used as defined in seqMeta.\n\n—\nYou are receiving this because you authored the thread.\nReply to this email directly, view it on GitHub<https://github.com/rmkoesterer/uga/issues/21#issuecomment-247675764>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AUXD3HdlUQ_T_11Y8Tvkq9Uqt9yW2KYKks5qquIhgaJpZM4J-RGE>.\n"}}
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