Package index • cbioportalR

Authentication

set_cbioportal_db(): Connect to cBioPortal DB

get_cbioportal_token(): Get cBioPortal Access Token

test_cbioportal_db(): Test the Database Connection Anytime During your R Session

Database Level

available_gene_panels(): Get Available Gene Panels For a Database

available_studies(): Get Metadata on All Available Studies in a Database

get_genes(): Get A List of Genes for a Specified Database

lookup_id(): Lookup all available information on what studies a sample ID or patient ID belongs to

Database or Study Level

available_profiles(): Get Available Genomic Profiles For a Study or Database

get_study_info(): Get Metadata on All Available Studies in Database or a Specified Study

Study Level

available_clinical_attributes(): Get all available clinical attribute IDs for a study

get_clinical_by_study(): Get all available clinical data for a specified study

get_mutations_by_study(): Get Mutations By Study ID

get_cna_by_study(): Get CNA By Study

get_fusions_by_study() get_structural_variants_by_study(): Get Fusions By Study

get_segments_by_study(): Get Copy Number Segmentation Data By Study

available_samples(): Get All Sample IDs in a Study

available_patients(): Get All Patient IDs in a Study

available_sample_lists(): Get All Sample Lists Available For a Study

get_genetics_by_study(): Get All Genomic Information By Study

Sample Level

get_clinical_by_sample(): Get clinical data by attribute, study ID and sample ID

get_mutations_by_sample(): Get Mutations By Sample ID

get_cna_by_sample(): Get CNA By Sample ID

get_fusions_by_sample() get_structural_variants_by_sample(): Get Fusions By Sample ID

get_segments_by_sample(): Get Copy Number Segmentation Data By Sample ID

get_genetics_by_sample(): Get All Genomic Information By Sample IDs

get_panel_by_sample(): Get Gene Panel by study ID and sample ID

Gene & Gene Panel Level

get_alias(): Get Gene Name Alias for a Given Hugo Symbol

get_entrez_id(): Get Entrez Gene ID for a given set of Hugo Symbols

get_gene_panel(): Retrieve Genes Included For a Specified Panel ID

get_hugo_symbol(): Get Hugo Symbol for a given set of Entrez IDs

Patient Level

get_samples_by_patient(): Get sample IDs for a given set of patient IDs

get_clinical_by_patient(): Get clinical data by attribute, study ID and patient ID

Data

impact_gene_info: IMPACT Gene Meta Data