{"action":"opened","issue":{"url":"https://api.github.com/repos/thibautjombart/adegenet/issues/225","repository_url":"https://api.github.com/repos/thibautjombart/adegenet","labels_url":"https://api.github.com/repos/thibautjombart/adegenet/issues/225/labels{/name}","comments_url":"https://api.github.com/repos/thibautjombart/adegenet/issues/225/comments","events_url":"https://api.github.com/repos/thibautjombart/adegenet/issues/225/events","html_url":"https://github.com/thibautjombart/adegenet/issues/225","id":299342075,"number":225,"title":"\".\" not recognised as a missing character when creating genlight object","user":{"login":"suzyhh","id":36733421,"avatar_url":"https://avatars0.githubusercontent.com/u/36733421?v=4","gravatar_id":"","url":"https://api.github.com/users/suzyhh","html_url":"https://github.com/suzyhh","followers_url":"https://api.github.com/users/suzyhh/followers","following_url":"https://api.github.com/users/suzyhh/following{/other_user}","gists_url":"https://api.github.com/users/suzyhh/gists{/gist_id}","starred_url":"https://api.github.com/users/suzyhh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/suzyhh/subscriptions","organizations_url":"https://api.github.com/users/suzyhh/orgs","repos_url":"https://api.github.com/users/suzyhh/repos","events_url":"https://api.github.com/users/suzyhh/events{/privacy}","received_events_url":"https://api.github.com/users/suzyhh/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-02-22T12:51:58Z","updated_at":"2018-02-22T12:51:58Z","closed_at":null,"author_association":"NONE","body":"Hiya,\r\n\r\nI'm using read.vcf (pegas) to read a multisample VCF (ms) into R and then creating a genlight object:\r\n\r\nms<-read.vcf(\"multisample.vcf\")\r\nms.genlight.<-new(\"genlight\" , ms , ploidy=1 , NA.char=\" . \")\r\n\r\nAs read.vcf replaces missing data with a dot, I'm trying to get this recognised when I convert to genlight, however I never seem to be successful and the dots are counted as real data when I make my genlight object.\r\n\r\nI've tried escaping before the dot as well (NA.char=\"\\\\.\") but this also fails.\r\n\r\nCan you advise on how to fix this issue? If not - are there any other methods you recommend for importing and converting a multisample VCF?\r\n\r\nThanks,\r\nSuzy"}}
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