{"action":"created","issue":{"url":"https://api.github.com/repos/QTCAT/qtcat/issues/7","repository_url":"https://api.github.com/repos/QTCAT/qtcat","labels_url":"https://api.github.com/repos/QTCAT/qtcat/issues/7/labels{/name}","comments_url":"https://api.github.com/repos/QTCAT/qtcat/issues/7/comments","events_url":"https://api.github.com/repos/QTCAT/qtcat/issues/7/events","html_url":"https://github.com/QTCAT/qtcat/issues/7","id":153427058,"number":7,"title":"How to handle ambiguity codes (and other queries)","user":{"login":"nstjhp","id":5261752,"avatar_url":"https://avatars.githubusercontent.com/u/5261752?v=3","gravatar_id":"","url":"https://api.github.com/users/nstjhp","html_url":"https://github.com/nstjhp","followers_url":"https://api.github.com/users/nstjhp/followers","following_url":"https://api.github.com/users/nstjhp/following{/other_user}","gists_url":"https://api.github.com/users/nstjhp/gists{/gist_id}","starred_url":"https://api.github.com/users/nstjhp/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nstjhp/subscriptions","organizations_url":"https://api.github.com/users/nstjhp/orgs","repos_url":"https://api.github.com/users/nstjhp/repos","events_url":"https://api.github.com/users/nstjhp/events{/privacy}","received_events_url":"https://api.github.com/users/nstjhp/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2016-05-06T10:51:56Z","updated_at":"2016-05-13T12:34:29Z","closed_at":null,"body":"Hi Jonas, in the real data set we were testing qtcat on yesterday we found a few problems that I do not know how to handle.\r\n\r\n1. \r\nWe have a great deal of ambiguity codes (K,R,M,Y etc.) called throughout the data in many different lines and marker positions - can the method behind qtcat adapt to when you don't just have ACGT?\r\n\r\n2. \r\nBefore this though we had to exclude about 80% of the data due to missing marker data - I see you have a PR on this - is that branch suitable for testing?\r\n\r\n3. \r\nEven after cleaning up the data to only get complete cases with no ambiguity codes (down to 0.2% of our original data!) we had a couple of markers where there were 3 possible alleles across the lines - I also wonder if this can be handled at some point? I show an example below:\r\n\r\nI made a tiny file (call it tmp.csv) to check that this was really the case and also found the warning message is slightly incorrect. \r\n```\r\nChromosome,Positions,Indiv1,Indiv2,Indiv3,Indiv4\r\n1,10,AA,CC,CC,GT\r\n1,420,AA,CC,GT,AA\r\n1,804,AA,AA,AG,AA\r\n1,942,AG,AA,GG,AG\r\n1,1122,CG,CG,CG,AA\r\n1,2434,TT,TT,CT,CT\r\n```\r\n\r\n```\r\nR> read.snpData(\"tmp.csv\",sep = \",\")\r\nwarning: Line 2 has more or less than two alleles and therefore the line is skipt\r\nwarning: Line 2 has more or less than two alleles and therefore the line is skipt\r\nwarning: Line 4 has more or less than two alleles and therefore the line is skipt\r\n```\r\n\r\nI think it should be lines 1,2 and 5 that are skipped based on what goes into the position slot of snpData.\r\n\r\nThank you for your time\r\n"},"comment":{"url":"https://api.github.com/repos/QTCAT/qtcat/issues/comments/219030507","html_url":"https://github.com/QTCAT/qtcat/issues/7#issuecomment-219030507","issue_url":"https://api.github.com/repos/QTCAT/qtcat/issues/7","id":219030507,"user":{"login":"nstjhp","id":5261752,"avatar_url":"https://avatars.githubusercontent.com/u/5261752?v=3","gravatar_id":"","url":"https://api.github.com/users/nstjhp","html_url":"https://github.com/nstjhp","followers_url":"https://api.github.com/users/nstjhp/followers","following_url":"https://api.github.com/users/nstjhp/following{/other_user}","gists_url":"https://api.github.com/users/nstjhp/gists{/gist_id}","starred_url":"https://api.github.com/users/nstjhp/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nstjhp/subscriptions","organizations_url":"https://api.github.com/users/nstjhp/orgs","repos_url":"https://api.github.com/users/nstjhp/repos","events_url":"https://api.github.com/users/nstjhp/events{/privacy}","received_events_url":"https://api.github.com/users/nstjhp/received_events","type":"User","site_admin":false},"created_at":"2016-05-13T12:34:29Z","updated_at":"2016-05-13T12:34:29Z","body":"Thanks for the info I'll take a look at the `as.snpData` as that sounds potentially promising for what we can get out of other programs.\r\n\r\nIf that is how it works then I will probably try increasing `B` to be more sure of which are the true candidates. I ran the default qtcat over the dataset 5 times and different SNPs were pulled out 1-5 times which is why I was a little concerned. Certainly the ones that came up in every run seem to be good candidates to move forward with. And the number of clusters between runs similarly varied e.g. between 6 and 13 clusters sometimes using the same data. What is controlling the threshold you referred to? It seems it could be useful to check how far above it the various QTCs are.\r\n\r\nAlso, to learn more about the method (and maybe save so many queries), could you please give me an indication of when the paper might be out? I can email you if you prefer that to be kept private."}}