{"action":"created","issue":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1102","repository_url":"https://api.github.com/repos/cBioPortal/cbioportal","labels_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1102/labels{/name}","comments_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1102/comments","events_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1102/events","html_url":"https://github.com/cBioPortal/cbioportal/issues/1102","id":150852625,"number":1102,"title":"FUSION data is not retrieved by new data manager/oncoprint","user":{"login":"pieterlukasse","id":2900303,"avatar_url":"https://avatars.githubusercontent.com/u/2900303?v=3","gravatar_id":"","url":"https://api.github.com/users/pieterlukasse","html_url":"https://github.com/pieterlukasse","followers_url":"https://api.github.com/users/pieterlukasse/followers","following_url":"https://api.github.com/users/pieterlukasse/following{/other_user}","gists_url":"https://api.github.com/users/pieterlukasse/gists{/gist_id}","starred_url":"https://api.github.com/users/pieterlukasse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pieterlukasse/subscriptions","organizations_url":"https://api.github.com/users/pieterlukasse/orgs","repos_url":"https://api.github.com/users/pieterlukasse/repos","events_url":"https://api.github.com/users/pieterlukasse/events{/privacy}","received_events_url":"https://api.github.com/users/pieterlukasse/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/cBioPortal/cbioportal/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":{"login":"pieterlukasse","id":2900303,"avatar_url":"https://avatars.githubusercontent.com/u/2900303?v=3","gravatar_id":"","url":"https://api.github.com/users/pieterlukasse","html_url":"https://github.com/pieterlukasse","followers_url":"https://api.github.com/users/pieterlukasse/followers","following_url":"https://api.github.com/users/pieterlukasse/following{/other_user}","gists_url":"https://api.github.com/users/pieterlukasse/gists{/gist_id}","starred_url":"https://api.github.com/users/pieterlukasse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pieterlukasse/subscriptions","organizations_url":"https://api.github.com/users/pieterlukasse/orgs","repos_url":"https://api.github.com/users/pieterlukasse/repos","events_url":"https://api.github.com/users/pieterlukasse/events{/privacy}","received_events_url":"https://api.github.com/users/pieterlukasse/received_events","type":"User","site_admin":false},"milestone":null,"comments":6,"created_at":"2016-04-25T13:11:34Z","updated_at":"2016-05-12T09:53:50Z","closed_at":null,"body":"Fusion data is present in some studies, like prostate cancer studies (e.g. [see this query](http://www.cbioportal.org/index.do?cancer_study_list=prad_su2c_2015&cancer_study_id=prad_su2c_2015&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=prad_su2c_2015_mutations&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=prad_su2c_2015_gistic&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=prad_su2c_2015_rna_seq_mrna_median_Zscores&Z_SCORE_THRESHOLD=2.0&data_priority=0&case_set_id=prad_su2c_2015_cnaseq&case_ids=&patient_case_select=sample&gene_set_choice=prostate-cancer%3A-ar-signaling-%2810-genes%29&gene_list=TMPRSS2+ERG+SLC45A3+ETV1&clinical_param_selection=null&tab_index=tab_visualize&Action=Submit))\r\n\r\nThe documentation for the *old* and *new* ways of loading data both fail to describe how to make correct fusion data files that will also successfully work in the oncoprint display. The problem seems to be due to the fact that the new data manager layer used by oncoprint expects the **fusion data** to be part of the **mutations** genetic profile. But making a meta file as described in the documentation makes a new separate genetic profile and loads all fusion data into this other genetic profile. \r\n\r\nPossible solutions:\r\n- adjust loader code at `ImportProfileData` to exceptionally load Fusion data into the genetic profile of mutations. This means mutation data should also always be loaded first.\r\n- OR adjust oncoprint/data manager layer to retrieve the data from the Fusion genetic profile. This can be a confusing change as the Fusion genetic profile will have to be \"visible\" in the query page. Also many other places in the application that retrieve mutation data will need to be adjusted to also consider the extra Fusion genetic profile...\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/comments/218711703","html_url":"https://github.com/cBioPortal/cbioportal/issues/1102#issuecomment-218711703","issue_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1102","id":218711703,"user":{"login":"pieterlukasse","id":2900303,"avatar_url":"https://avatars.githubusercontent.com/u/2900303?v=3","gravatar_id":"","url":"https://api.github.com/users/pieterlukasse","html_url":"https://github.com/pieterlukasse","followers_url":"https://api.github.com/users/pieterlukasse/followers","following_url":"https://api.github.com/users/pieterlukasse/following{/other_user}","gists_url":"https://api.github.com/users/pieterlukasse/gists{/gist_id}","starred_url":"https://api.github.com/users/pieterlukasse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pieterlukasse/subscriptions","organizations_url":"https://api.github.com/users/pieterlukasse/orgs","repos_url":"https://api.github.com/users/pieterlukasse/repos","events_url":"https://api.github.com/users/pieterlukasse/events{/privacy}","received_events_url":"https://api.github.com/users/pieterlukasse/received_events","type":"User","site_admin":false},"created_at":"2016-05-12T09:53:50Z","updated_at":"2016-05-12T09:53:50Z","body":"part of it (at least allowing multiple mutation files in the loader) is solved in #1212 "}}