{"action":"created","issue":{"url":"https://api.github.com/repos/ding-lab/msisensor/issues/20","repository_url":"https://api.github.com/repos/ding-lab/msisensor","labels_url":"https://api.github.com/repos/ding-lab/msisensor/issues/20/labels{/name}","comments_url":"https://api.github.com/repos/ding-lab/msisensor/issues/20/comments","events_url":"https://api.github.com/repos/ding-lab/msisensor/issues/20/events","html_url":"https://github.com/ding-lab/msisensor/issues/20","id":346789440,"node_id":"MDU6SXNzdWUzNDY3ODk0NDA=","number":20,"title":"MSI score Plot","user":{"login":"Jemkon","id":32181378,"node_id":"MDQ6VXNlcjMyMTgxMzc4","avatar_url":"https://avatars1.githubusercontent.com/u/32181378?v=4","gravatar_id":"","url":"https://api.github.com/users/Jemkon","html_url":"https://github.com/Jemkon","followers_url":"https://api.github.com/users/Jemkon/followers","following_url":"https://api.github.com/users/Jemkon/following{/other_user}","gists_url":"https://api.github.com/users/Jemkon/gists{/gist_id}","starred_url":"https://api.github.com/users/Jemkon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Jemkon/subscriptions","organizations_url":"https://api.github.com/users/Jemkon/orgs","repos_url":"https://api.github.com/users/Jemkon/repos","events_url":"https://api.github.com/users/Jemkon/events{/privacy}","received_events_url":"https://api.github.com/users/Jemkon/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-08-01T22:14:37Z","updated_at":"2018-08-02T11:36:37Z","closed_at":null,"author_association":"NONE","body":"Hello,\r\n\r\nI have got the output files for tumor only BAMs. I would like to run Plot.R script. But I dont know which file I should use as input to Plot.R.\r\n\r\nHere are 3 my outfiles:\r\ntumorBam.MSI\r\ntumorBaM.MSI_dis\r\ntumorBam.MSI_somatic\r\n\r\nMany thanks,"},"comment":{"url":"https://api.github.com/repos/ding-lab/msisensor/issues/comments/409896836","html_url":"https://github.com/ding-lab/msisensor/issues/20#issuecomment-409896836","issue_url":"https://api.github.com/repos/ding-lab/msisensor/issues/20","id":409896836,"node_id":"MDEyOklzc3VlQ29tbWVudDQwOTg5NjgzNg==","user":{"login":"ZhaoDanOnGitHub","id":31035928,"node_id":"MDQ6VXNlcjMxMDM1OTI4","avatar_url":"https://avatars0.githubusercontent.com/u/31035928?v=4","gravatar_id":"","url":"https://api.github.com/users/ZhaoDanOnGitHub","html_url":"https://github.com/ZhaoDanOnGitHub","followers_url":"https://api.github.com/users/ZhaoDanOnGitHub/followers","following_url":"https://api.github.com/users/ZhaoDanOnGitHub/following{/other_user}","gists_url":"https://api.github.com/users/ZhaoDanOnGitHub/gists{/gist_id}","starred_url":"https://api.github.com/users/ZhaoDanOnGitHub/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ZhaoDanOnGitHub/subscriptions","organizations_url":"https://api.github.com/users/ZhaoDanOnGitHub/orgs","repos_url":"https://api.github.com/users/ZhaoDanOnGitHub/repos","events_url":"https://api.github.com/users/ZhaoDanOnGitHub/events{/privacy}","received_events_url":"https://api.github.com/users/ZhaoDanOnGitHub/received_events","type":"User","site_admin":false},"created_at":"2018-08-02T11:36:37Z","updated_at":"2018-08-02T11:36:37Z","author_association":"NONE","body":"Hello,\r\n\r\nThe function of drawing is for the sample group, not for a single sample.\r\nYou can refer to the example in the test folder: msi_score_and_status_list and msi_score_only_list. Each line is a sample of msicore and status or msiscore only. Msiscore is obtained form tumorBam.MSI.\r\nFor example, there are two samlpes: sample_1 and sample_2. We will get 3 outfiles for each sample. For sample_1, we will get sample_1_output, sample_1_output_dis,  sample_1_output_somatic. And for sample_2, 3 outfiles are sample_2_output, sample_2_output_dis and sample_2_output_somatic. \r\nFor sample_1, outfile sample_1_output is as follow:\r\nTotal_Number_of_Sites   Number_of_Somatic_Sites %\r\n12015   3425    28.51\r\nFor samlple_2, outfile sample_2_output is as follow:\r\nTotal_Number_of_Sites   Number_of_Somatic_Sites %\r\n9219    33  0.36\r\nThen we extract msiscores from sample_1 and sample_2. If you have MSI status, msi_score_and _status_list file is as follow:\r\n28.51 MSI\r\n0.36 MSS\r\nIf you don’t have MSI status, msi_score_only_list is as follow:\r\n28.51\r\n0.36 \r\nYou can use msi_score_and_status_list or msi_score_onlu_list as input for Plot.R.\r\n\r\nThanks"}}
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