{"action":"opened","issue":{"url":"https://api.github.com/repos/diazlab/CONICS/issues/1","repository_url":"https://api.github.com/repos/diazlab/CONICS","labels_url":"https://api.github.com/repos/diazlab/CONICS/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/diazlab/CONICS/issues/1/comments","events_url":"https://api.github.com/repos/diazlab/CONICS/issues/1/events","html_url":"https://github.com/diazlab/CONICS/issues/1","id":314346936,"number":1,"title":"extract the samples with CNV","user":{"login":"wasqqdyx","id":15790040,"avatar_url":"https://avatars1.githubusercontent.com/u/15790040?v=4","gravatar_id":"","url":"https://api.github.com/users/wasqqdyx","html_url":"https://github.com/wasqqdyx","followers_url":"https://api.github.com/users/wasqqdyx/followers","following_url":"https://api.github.com/users/wasqqdyx/following{/other_user}","gists_url":"https://api.github.com/users/wasqqdyx/gists{/gist_id}","starred_url":"https://api.github.com/users/wasqqdyx/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wasqqdyx/subscriptions","organizations_url":"https://api.github.com/users/wasqqdyx/orgs","repos_url":"https://api.github.com/users/wasqqdyx/repos","events_url":"https://api.github.com/users/wasqqdyx/events{/privacy}","received_events_url":"https://api.github.com/users/wasqqdyx/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-04-14T17:31:41Z","updated_at":"2018-04-14T17:31:41Z","closed_at":null,"author_association":"NONE","body":"Thanks for the fantastic tool! I am currently using it on my single cell data. \r\n\r\nHowever, I found some inconsistencies when I try to extract the cells with CNV. \r\n\r\nFirst, I used this output \"bin_mat=binarizeMatrix(redu,normal,tumor,0.8); cells1<-apply(bin_mat,1, sum)\" . I suppose the cells1 with higher value are cells with CNV. \r\n\r\nOn the other hand, I also tried to use the heatmap generated by \"plot1<plotBinaryMat(bin_mat,patients,normal,tumor,patient=patients); CNVs= cutree(plot1$tree_col,k=3)\". Then I took the cluster that showed with CNVs in heatmap. Surprisingly, the cells differed greatly with the cells1 that I got above. \r\n\r\nI feel so confused about it. Could you give some information? Which one is right or how to get the cells with CNV?\r\n\r\nThanks a lot!\r\n\r\n"}}
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