{"action":"created","issue":{"url":"https://api.github.com/repos/mgalardini/pyseer/issues/37","repository_url":"https://api.github.com/repos/mgalardini/pyseer","labels_url":"https://api.github.com/repos/mgalardini/pyseer/issues/37/labels{/name}","comments_url":"https://api.github.com/repos/mgalardini/pyseer/issues/37/comments","events_url":"https://api.github.com/repos/mgalardini/pyseer/issues/37/events","html_url":"https://github.com/mgalardini/pyseer/issues/37","id":321582710,"number":37,"title":"Lineage association question","user":{"login":"rafarios50","id":11218027,"avatar_url":"https://avatars3.githubusercontent.com/u/11218027?v=4","gravatar_id":"","url":"https://api.github.com/users/rafarios50","html_url":"https://github.com/rafarios50","followers_url":"https://api.github.com/users/rafarios50/followers","following_url":"https://api.github.com/users/rafarios50/following{/other_user}","gists_url":"https://api.github.com/users/rafarios50/gists{/gist_id}","starred_url":"https://api.github.com/users/rafarios50/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rafarios50/subscriptions","organizations_url":"https://api.github.com/users/rafarios50/orgs","repos_url":"https://api.github.com/users/rafarios50/repos","events_url":"https://api.github.com/users/rafarios50/events{/privacy}","received_events_url":"https://api.github.com/users/rafarios50/received_events","type":"User","site_admin":false},"labels":[{"id":699909063,"url":"https://api.github.com/repos/mgalardini/pyseer/labels/question","name":"question","color":"cc317c","default":true}],"state":"closed","locked":false,"assignee":{"login":"johnlees","id":6331837,"avatar_url":"https://avatars1.githubusercontent.com/u/6331837?v=4","gravatar_id":"","url":"https://api.github.com/users/johnlees","html_url":"https://github.com/johnlees","followers_url":"https://api.github.com/users/johnlees/followers","following_url":"https://api.github.com/users/johnlees/following{/other_user}","gists_url":"https://api.github.com/users/johnlees/gists{/gist_id}","starred_url":"https://api.github.com/users/johnlees/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/johnlees/subscriptions","organizations_url":"https://api.github.com/users/johnlees/orgs","repos_url":"https://api.github.com/users/johnlees/repos","events_url":"https://api.github.com/users/johnlees/events{/privacy}","received_events_url":"https://api.github.com/users/johnlees/received_events","type":"User","site_admin":false},"assignees":[{"login":"johnlees","id":6331837,"avatar_url":"https://avatars1.githubusercontent.com/u/6331837?v=4","gravatar_id":"","url":"https://api.github.com/users/johnlees","html_url":"https://github.com/johnlees","followers_url":"https://api.github.com/users/johnlees/followers","following_url":"https://api.github.com/users/johnlees/following{/other_user}","gists_url":"https://api.github.com/users/johnlees/gists{/gist_id}","starred_url":"https://api.github.com/users/johnlees/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/johnlees/subscriptions","organizations_url":"https://api.github.com/users/johnlees/orgs","repos_url":"https://api.github.com/users/johnlees/repos","events_url":"https://api.github.com/users/johnlees/events{/privacy}","received_events_url":"https://api.github.com/users/johnlees/received_events","type":"User","site_admin":false}],"milestone":null,"comments":4,"created_at":"2018-05-09T14:00:14Z","updated_at":"2018-05-17T13:45:45Z","closed_at":"2018-05-11T16:51:35Z","author_association":"NONE","body":"Good day,\r\n\r\nI wanted to know if some results that Im obtain, and which wasnt expected could be fine or if there might be some issu with my approach and use of pyseer.\r\n\r\nI have a set of isolates already classified into 5 different populations (lineages) of different sizes (number of isolates).\r\n\r\nAnd wanted to know if there were some kmers associated to the lineage, which could explain why the populations were different.\r\n\r\nTo do so I used fms-lite to count the kmers and mash to obtain the distance matrix. Then I did 5 different analysis, one for each population, setting the pheno file with 1 if that isolate belonged to the queried population (case) and 0 if not (control), using the lineage option, given the labels for each population and forcing the use of continuous phenotype (as binary would perfectly separate the data and no regression was done).\r\n\r\nIn each experiment, the lineage_effects.txt file associated the corresponded population as the most important to the phenotype (expected result). But when looking into the kmers, in one case, there were no kmers related to the population.\r\n\r\nMy question is: What could be happening there that no kmer was found to be associated to the expected population, something that didnt happen to the other experiments?\r\n\r\nThank you,\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/mgalardini/pyseer/issues/comments/389871461","html_url":"https://github.com/mgalardini/pyseer/issues/37#issuecomment-389871461","issue_url":"https://api.github.com/repos/mgalardini/pyseer/issues/37","id":389871461,"user":{"login":"rafarios50","id":11218027,"avatar_url":"https://avatars3.githubusercontent.com/u/11218027?v=4","gravatar_id":"","url":"https://api.github.com/users/rafarios50","html_url":"https://github.com/rafarios50","followers_url":"https://api.github.com/users/rafarios50/followers","following_url":"https://api.github.com/users/rafarios50/following{/other_user}","gists_url":"https://api.github.com/users/rafarios50/gists{/gist_id}","starred_url":"https://api.github.com/users/rafarios50/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rafarios50/subscriptions","organizations_url":"https://api.github.com/users/rafarios50/orgs","repos_url":"https://api.github.com/users/rafarios50/repos","events_url":"https://api.github.com/users/rafarios50/events{/privacy}","received_events_url":"https://api.github.com/users/rafarios50/received_events","type":"User","site_admin":false},"created_at":"2018-05-17T13:45:45Z","updated_at":"2018-05-17T13:45:45Z","author_association":"NONE","body":"Thank you for the fix, but unfortunately, it didnt work with my data.\r\n\r\nAfter filtering the kmers accordingly to the threshold by the count_patterns.py script, no kmer was found to be related to the lineage im interested in.\r\n\r\nWouldn't it mean that this lineage is characterized as not having the other kmers associated to the other lineages (something like an inverse proportion)? Would it be possible to conclude that with this kind of analysis?\r\n\r\n"}}
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