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1.1.10","description":"","creator":{"login":"anpefi","id":3452676,"avatar_url":"https://avatars.githubusercontent.com/u/3452676?v=3","gravatar_id":"","url":"https://api.github.com/users/anpefi","html_url":"https://github.com/anpefi","followers_url":"https://api.github.com/users/anpefi/followers","following_url":"https://api.github.com/users/anpefi/following{/other_user}","gists_url":"https://api.github.com/users/anpefi/gists{/gist_id}","starred_url":"https://api.github.com/users/anpefi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/anpefi/subscriptions","organizations_url":"https://api.github.com/users/anpefi/orgs","repos_url":"https://api.github.com/users/anpefi/repos","events_url":"https://api.github.com/users/anpefi/events{/privacy}","received_events_url":"https://api.github.com/users/anpefi/received_events","type":"User","site_admin":false},"open_issues":3,"closed_issues":0,"state":"open","created_at":"2015-12-09T22:13:05Z","updated_at":"2016-02-08T07:04:26Z","due_on":null,"closed_at":null},"comments":0,"created_at":"2015-12-09T22:23:41Z","updated_at":"2016-07-05T11:05:49Z","closed_at":null,"body":"This is the issue [#6262](https://r-forge.r-project.org/tracker/index.php?func=detail&aid=6262&group_id=1422&atid=5292) in the R-Forge support tracker "},"comment":{"url":"https://api.github.com/repos/anpefi/msap/issues/comments/230449851","html_url":"https://github.com/anpefi/msap/issues/2#issuecomment-230449851","issue_url":"https://api.github.com/repos/anpefi/msap/issues/2","id":230449851,"user":{"login":"anpefi","id":3452676,"avatar_url":"https://avatars.githubusercontent.com/u/3452676?v=3","gravatar_id":"","url":"https://api.github.com/users/anpefi","html_url":"https://github.com/anpefi","followers_url":"https://api.github.com/users/anpefi/followers","following_url":"https://api.github.com/users/anpefi/following{/other_user}","gists_url":"https://api.github.com/users/anpefi/gists{/gist_id}","starred_url":"https://api.github.com/users/anpefi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/anpefi/subscriptions","organizations_url":"https://api.github.com/users/anpefi/orgs","repos_url":"https://api.github.com/users/anpefi/repos","events_url":"https://api.github.com/users/anpefi/events{/privacy}","received_events_url":"https://api.github.com/users/anpefi/received_events","type":"User","site_admin":false},"created_at":"2016-07-05T11:05:49Z","updated_at":"2016-07-05T11:05:49Z","body":"This bug has been reported again by mail.\r\nIt happens when the dataset yields very low number of MSL with an high proportion of NAs. In that cases when the distance matrix is built it happens that some pairs of individuals **cannot be compared as they are at least one NA across all loci compared, yielding a NA in the matrix**. \r\n\r\nBy using njs() instead of nj() you can do the clustering because it is an algortithm designed for incomplete matrices. However, the PCoA cannot be done as, as far I know, there is not any algorithm allowing for working with missing data. \r\n\r\nI need to think what is the best way to address this issue and then implement it, and it will take some time. Probably by using a different distance or any heuristic way to give uninformative states a distance. **Suggestions are welcome about this**.\r\n\r\nAn alternative workaround, **if you could assume no (large) genetic differences between individuals across all the dataset** then you could assume that 0/0 patterns are much more probable to be caused by hemimethylation of the target than by mutation causing a lack of the target **and then consider them as methylated states (1) instead of missing (NA).** In this case (no.bands=\"h\") you can run the full analysis. "}}
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