{"action":"created","issue":{"url":"https://api.github.com/repos/PoisonAlien/maftools/issues/149","repository_url":"https://api.github.com/repos/PoisonAlien/maftools","labels_url":"https://api.github.com/repos/PoisonAlien/maftools/issues/149/labels{/name}","comments_url":"https://api.github.com/repos/PoisonAlien/maftools/issues/149/comments","events_url":"https://api.github.com/repos/PoisonAlien/maftools/issues/149/events","html_url":"https://github.com/PoisonAlien/maftools/issues/149","id":325324199,"number":149,"title":"Can't open MAF file","user":{"login":"kvn95ss","id":32951653,"avatar_url":"https://avatars3.githubusercontent.com/u/32951653?v=4","gravatar_id":"","url":"https://api.github.com/users/kvn95ss","html_url":"https://github.com/kvn95ss","followers_url":"https://api.github.com/users/kvn95ss/followers","following_url":"https://api.github.com/users/kvn95ss/following{/other_user}","gists_url":"https://api.github.com/users/kvn95ss/gists{/gist_id}","starred_url":"https://api.github.com/users/kvn95ss/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kvn95ss/subscriptions","organizations_url":"https://api.github.com/users/kvn95ss/orgs","repos_url":"https://api.github.com/users/kvn95ss/repos","events_url":"https://api.github.com/users/kvn95ss/events{/privacy}","received_events_url":"https://api.github.com/users/kvn95ss/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":10,"created_at":"2018-05-22T14:37:25Z","updated_at":"2018-05-23T07:51:42Z","closed_at":null,"author_association":"NONE","body":"I've converted wAnnovar output into MAF using annovarToMaf, then I then wrote it into a file (output.maf).\r\nWhen I tried to open the file again using read.maf(), I get the following error -\r\n\r\n> maf=read.maf(\"output.maf\")\r\nreading maf..\r\nNOTE: Removed 34 duplicated variants\r\nsilent variants: 245\r\n        ID   N\r\n1: Samples   6\r\n2: 3'Flank   3\r\n3:   3'UTR   3\r\n4:     IGR  12\r\n5:  Intron 204\r\n6:     RNA  23\r\nSummarizing..\r\nError in dcast.data.table(data = vc, formula = Tumor_Sample_Barcode ~  : \r\n  Can not cast an empty data.table\r\n\r\nAny idea what's going on? Why am I not able to import the file?"},"comment":{"url":"https://api.github.com/repos/PoisonAlien/maftools/issues/comments/391254387","html_url":"https://github.com/PoisonAlien/maftools/issues/149#issuecomment-391254387","issue_url":"https://api.github.com/repos/PoisonAlien/maftools/issues/149","id":391254387,"user":{"login":"ShixiangWang","id":25057508,"avatar_url":"https://avatars1.githubusercontent.com/u/25057508?v=4","gravatar_id":"","url":"https://api.github.com/users/ShixiangWang","html_url":"https://github.com/ShixiangWang","followers_url":"https://api.github.com/users/ShixiangWang/followers","following_url":"https://api.github.com/users/ShixiangWang/following{/other_user}","gists_url":"https://api.github.com/users/ShixiangWang/gists{/gist_id}","starred_url":"https://api.github.com/users/ShixiangWang/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ShixiangWang/subscriptions","organizations_url":"https://api.github.com/users/ShixiangWang/orgs","repos_url":"https://api.github.com/users/ShixiangWang/repos","events_url":"https://api.github.com/users/ShixiangWang/events{/privacy}","received_events_url":"https://api.github.com/users/ShixiangWang/received_events","type":"User","site_admin":false},"created_at":"2018-05-23T07:51:42Z","updated_at":"2018-05-23T07:51:42Z","author_association":"NONE","body":"@kvn95ss  You can run \r\n```\r\n?read.maf\r\n```\r\n\r\nto see the `vc_nonSyn` argument.\r\n\r\nIt says\r\n\r\n> NULL. Provide manual list of variant classifications to be considered as non-synonymous. Rest will be considered as silent variants. Default uses Variant Classifications with High/Moderate variant consequences. http://asia.ensembl.org/Help/Glossary?id=535: \"Frame_Shift_Del\", \"Frame_Shift_Ins\", \"Splice_Site\", \"Translation_Start_Site\",\"Nonsense_Mutation\", \"Nonstop_Mutation\", \"In_Frame_Del\",\"In_Frame_Ins\", \"Missense_Mutation\"\r\n\r\nCould you try \r\n\r\n```\r\nread.maf(\"SNP_in_cn.maf\", vc_nonSyn=c(\"3'Flank\", \"3'UTR\",  \"IGR\", \" Intron\",  \"RNA\"))\r\n```\r\n\r\nI have not test the code.  \r\n\r\n```\r\nvc_nonSyn=c(\"3'Flank\", \"3'UTR\",  \"IGR\", \" Intron\",  \"RNA\")\r\n``` \r\n\r\nmaybe is\r\n\r\n```\r\nvc_nonSyn=list(\"3'Flank\", \"3'UTR\",  \"IGR\", \" Intron\",  \"RNA\")\r\n```"}}
{"actor":{"display_login":"ShixiangWang"}}