{"action":"created","issue":{"url":"https://api.github.com/repos/PoisonAlien/maftools/issues/146","repository_url":"https://api.github.com/repos/PoisonAlien/maftools","labels_url":"https://api.github.com/repos/PoisonAlien/maftools/issues/146/labels{/name}","comments_url":"https://api.github.com/repos/PoisonAlien/maftools/issues/146/comments","events_url":"https://api.github.com/repos/PoisonAlien/maftools/issues/146/events","html_url":"https://github.com/PoisonAlien/maftools/issues/146","id":322383595,"number":146,"title":"plotApobecDiff error with maftools_1.4.28 and  maftools_1.6.05","user":{"login":"jeffchen2000","id":39199501,"avatar_url":"https://avatars0.githubusercontent.com/u/39199501?v=4","gravatar_id":"","url":"https://api.github.com/users/jeffchen2000","html_url":"https://github.com/jeffchen2000","followers_url":"https://api.github.com/users/jeffchen2000/followers","following_url":"https://api.github.com/users/jeffchen2000/following{/other_user}","gists_url":"https://api.github.com/users/jeffchen2000/gists{/gist_id}","starred_url":"https://api.github.com/users/jeffchen2000/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeffchen2000/subscriptions","organizations_url":"https://api.github.com/users/jeffchen2000/orgs","repos_url":"https://api.github.com/users/jeffchen2000/repos","events_url":"https://api.github.com/users/jeffchen2000/events{/privacy}","received_events_url":"https://api.github.com/users/jeffchen2000/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-05-11T17:59:48Z","updated_at":"2018-05-12T07:50:35Z","closed_at":null,"author_association":"NONE","body":"> laml.tnm=trinucleotideMatrix(maf = laml, ref_genome = 'hg19.fa',add = TRUE, ignoreChr = c('X','Y','MT'), useSyn = TRUE)\r\nreading hg19.fa (this might take few minutes)..\r\nExtracting 5' and 3' adjacent bases..\r\nExtracting +/- 20bp around mutated bases for background C>T estimation..\r\nEstimating APOBEC enrichment scores.. \r\nPerforming one-way Fisher's test for APOBEC enrichment..\r\nAPOBEC related mutations are enriched in 81.818% of samples (APOBEC enrichment score > 2 ; 9 of 11 samples)\r\nCreating mutation matrix..\r\nmatrix of dimension 11x96\r\n> plotApobecDiff(tnm = laml.tnm, maf = laml)\r\nError in file.exists(anno) : invalid 'file' argument\r\n"},"comment":{"url":"https://api.github.com/repos/PoisonAlien/maftools/issues/comments/388537830","html_url":"https://github.com/PoisonAlien/maftools/issues/146#issuecomment-388537830","issue_url":"https://api.github.com/repos/PoisonAlien/maftools/issues/146","id":388537830,"user":{"login":"PoisonAlien","id":8164062,"avatar_url":"https://avatars1.githubusercontent.com/u/8164062?v=4","gravatar_id":"","url":"https://api.github.com/users/PoisonAlien","html_url":"https://github.com/PoisonAlien","followers_url":"https://api.github.com/users/PoisonAlien/followers","following_url":"https://api.github.com/users/PoisonAlien/following{/other_user}","gists_url":"https://api.github.com/users/PoisonAlien/gists{/gist_id}","starred_url":"https://api.github.com/users/PoisonAlien/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/PoisonAlien/subscriptions","organizations_url":"https://api.github.com/users/PoisonAlien/orgs","repos_url":"https://api.github.com/users/PoisonAlien/repos","events_url":"https://api.github.com/users/PoisonAlien/events{/privacy}","received_events_url":"https://api.github.com/users/PoisonAlien/received_events","type":"User","site_admin":false},"created_at":"2018-05-12T07:50:35Z","updated_at":"2018-05-12T07:50:35Z","author_association":"OWNER","body":"Hi,\r\nI have hard time tracking the issue. Was your maf read along with clinical data ? Is it possible to share your maf file?"}}
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