Get Copy Number Segmentation Data By Sample ID

Usage

get_segments_by_sample(
  sample_id = NULL,
  study_id = NULL,
  sample_study_pairs = NULL,
  base_url = NULL
)

Arguments

sample_id: a vector of sample IDs (character)
study_id: A string indicating the study ID from which to pull data. If no study ID, will guess the study ID based on your URL and inform. Only 1 study ID can be passed. If mutations/cna from more than 1 study needed, see sample_study_pairs
sample_study_pairs: A dataframe with columns: sample_id, study_id and molecular_profile_id (optional). Variations in capitalization of column names are accepted. This can be used in place of sample_id, study_id, molecular_profile_id arguments above if you need to pull samples from several different studies at once. If passed this will take overwrite sample_id, study_id, molecular_profile_id if also passed.
base_url: The database URL to query If NULL will default to URL set with set_cbioportal_db(<your_db>)

Value

A dataframe of CNA segments

Examples

# \dontrun{
set_cbioportal_db("public")
#> ✔ You are successfully connected!
#> ✔ base_url for this R session is now set to "www.cbioportal.org/api" 

get_segments_by_sample(sample_id = c("s_C_CAUWT7_P001_d"),
                 study_id = "prad_msk_2019")
#> The following parameters were used in query:
#> Study ID: "prad_msk_2019"
#> Molecular Profile ID: "Not Applicable"
#> Genes: "All available genes"
#> # A tibble: 47 × 10
#>    uniqueSampleKey  uniquePatientKey patientId  start    end segmentMean studyId
#>    <chr>            <chr>            <chr>      <int>  <int>       <dbl> <chr>  
#>  1 c19DX0NBVVdUN19… cF9DX0NBVVdUNzp… p_C_CAUW… 2.49e6 2.47e8      0.0479 prad_m…
#>  2 c19DX0NBVVdUN19… cF9DX0NBVVdUNzp… p_C_CAUW… 4.72e6 2.43e8     -0.0846 prad_m…
#>  3 c19DX0NBVVdUN19… cF9DX0NBVVdUNzp… p_C_CAUW… 1.45e6 3.65e7      0.054  prad_m…
#>  4 c19DX0NBVVdUN19… cF9DX0NBVVdUNzp… p_C_CAUW… 3.70e7 3.85e7     -0.297  prad_m…
#>  5 c19DX0NBVVdUN19… cF9DX0NBVVdUNzp… p_C_CAUW… 3.95e7 1.94e8      0.0539 prad_m…
#>  6 c19DX0NBVVdUN19… cF9DX0NBVVdUNzp… p_C_CAUW… 1.40e6 1.90e8     -0.087  prad_m…
#>  7 c19DX0NBVVdUN19… cF9DX0NBVVdUNzp… p_C_CAUW… 2.19e5 4.43e7      0.0672 prad_m…
#>  8 c19DX0NBVVdUN19… cF9DX0NBVVdUNzp… p_C_CAUW… 5.27e7 7.51e7     -0.267  prad_m…
#>  9 c19DX0NBVVdUN19… cF9DX0NBVVdUNzp… p_C_CAUW… 7.59e7 1.80e8      0.0921 prad_m…
#> 10 c19DX0NBVVdUN19… cF9DX0NBVVdUNzp… p_C_CAUW… 3.93e5 3.13e7     -0.121  prad_m…
#> # ℹ 37 more rows
#> # ℹ 3 more variables: sampleId <chr>, chromosome <chr>, numberOfProbes <int>
                 # }