Get Fusions By Study

Usage

get_fusions_by_study(
  study_id = NULL,
  molecular_profile_id = NULL,
  base_url = NULL
)

get_structural_variants_by_study(
  study_id = NULL,
  molecular_profile_id = NULL,
  base_url = NULL
)

Arguments

study_id: A study ID to query mutations. If NULL, guesses study ID based on molecular_profile_id.
molecular_profile_id: a molecular profile to query mutations. If NULL, guesses molecular_profile_id based on study ID.
base_url: The database URL to query If NULL will default to URL set with set_cbioportal_db(<your_db>)

Value

A dataframe of fusions

Examples

# \dontrun{
# These return the same results
get_fusions_by_study(molecular_profile_id = "prad_msk_2019_structural_variants")
#> ℹ Returning all data for the "prad_msk_2019_structural_variants" molecular profile in the "prad_msk_2019" study
#> # A tibble: 4 × 44
#>   uniqueSampleKey uniquePatientKey molecularProfileId sampleId patientId studyId
#>   <chr>           <chr>            <chr>              <chr>    <chr>     <chr>  
#> 1 c19DX0NBVVdUN1… cF9DX0NBVVdUNzp… prad_msk_2019_str… s_C_CAU… p_C_CAUW… prad_m…
#> 2 c19DX0RVNkVDQ1… cF9DX0RVNkVDQzp… prad_msk_2019_str… s_C_DU6… p_C_DU6E… prad_m…
#> 3 c19DX1ZDNlA5QV… cF9DX1ZDNlA5QTp… prad_msk_2019_str… s_C_VC6… p_C_VC6P… prad_m…
#> 4 c19DX1ZDNlA5QV… cF9DX1ZDNlA5QTp… prad_msk_2019_str… s_C_VC6… p_C_VC6P… prad_m…
#> # ℹ 38 more variables: site1EntrezGeneId <int>, site1HugoSymbol <chr>,
#> #   site1EnsemblTranscriptId <chr>, site1Chromosome <chr>, site1Position <int>,
#> #   site1Contig <chr>, site1Region <chr>, site1RegionNumber <int>,
#> #   site1Description <chr>, site2EntrezGeneId <int>, site2HugoSymbol <chr>,
#> #   site2EnsemblTranscriptId <chr>, site2Chromosome <chr>, site2Position <int>,
#> #   site2Contig <chr>, site2Region <chr>, site2RegionNumber <int>,
#> #   site2Description <chr>, site2EffectOnFrame <chr>, ncbiBuild <chr>, …

get_structural_variants_by_study(molecular_profile_id =
       "prad_msk_2019_structural_variants")
#> ℹ Returning all data for the "prad_msk_2019_structural_variants" molecular profile in the "prad_msk_2019" study
#> # A tibble: 4 × 44
#>   uniqueSampleKey uniquePatientKey molecularProfileId sampleId patientId studyId
#>   <chr>           <chr>            <chr>              <chr>    <chr>     <chr>  
#> 1 c19DX0NBVVdUN1… cF9DX0NBVVdUNzp… prad_msk_2019_str… s_C_CAU… p_C_CAUW… prad_m…
#> 2 c19DX0RVNkVDQ1… cF9DX0RVNkVDQzp… prad_msk_2019_str… s_C_DU6… p_C_DU6E… prad_m…
#> 3 c19DX1ZDNlA5QV… cF9DX1ZDNlA5QTp… prad_msk_2019_str… s_C_VC6… p_C_VC6P… prad_m…
#> 4 c19DX1ZDNlA5QV… cF9DX1ZDNlA5QTp… prad_msk_2019_str… s_C_VC6… p_C_VC6P… prad_m…
#> # ℹ 38 more variables: site1EntrezGeneId <int>, site1HugoSymbol <chr>,
#> #   site1EnsemblTranscriptId <chr>, site1Chromosome <chr>, site1Position <int>,
#> #   site1Contig <chr>, site1Region <chr>, site1RegionNumber <int>,
#> #   site1Description <chr>, site2EntrezGeneId <int>, site2HugoSymbol <chr>,
#> #   site2EnsemblTranscriptId <chr>, site2Chromosome <chr>, site2Position <int>,
#> #   site2Contig <chr>, site2Region <chr>, site2RegionNumber <int>,
#> #   site2Description <chr>, site2EffectOnFrame <chr>, ncbiBuild <chr>, …
       # }