Queries the CGDS API and returns available case lists for a specific cancer study.
A CGDS object (required)
cancer study ID (required)
Queries the CGDS API and returns available case lists for a specific cancer study. For example, a within a particular study, only some cases may have sequence data, and another subset of cases may have been sequenced and treated with a specific therapeutic protocol. Multiple case lists may be associated with each cancer study, and this method enables you to retrieve meta-data regarding all of these case lists.
A data.frame with five columns:
case_list_id: a unique ID used to identify the case list ID in subsequent interface calls. This is a human readable ID. For example, "gbm_tcga_all" identifies all cases profiles in the TCGA GBM study.
case_list_name: short name for the case list.
case_list_description: short description of the case list.
cancer_study_id: cancer study ID tied to this genetic profile. Will match the input cancer_study_id.
case_ids: space delimited list of all case IDs that make up this case list.
cBio Cancer Genomics Portal: http://www.cbioportal.org/
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# Create CGDS object mycgds = CGDS("http://www.cbioportal.org/") # Get list of cancer studies at server getCancerStudies(mycgds) # Get available case lists (collection of samples) for a given cancer study mycancerstudy = getCancerStudies(mycgds)[2,1] mycaselist = getCaseLists(mycgds,mycancerstudy)[1,1] # Get available genetic profiles mygeneticprofile = getGeneticProfiles(mycgds,mycancerstudy)[1,1] # Get data slices for a specified list of genes, genetic profile and case list getProfileData(mycgds,c('BRCA1','BRCA2'),mygeneticprofile,mycaselist)
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