Get Mutations By Sample ID

Usage

get_mutations_by_sample(
  sample_id = NULL,
  study_id = NULL,
  molecular_profile_id = NULL,
  sample_study_pairs = NULL,
  genes = NULL,
  panel = NULL,
  add_hugo = TRUE,
  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
molecular_profile_id: A string indicating the molecular profile ID from which to pull data. If ID supplied, will guess the molecular profile ID based on the study ID. Only 1 molecular profile ID can be passed. If mutations 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.
genes: A vector of Entrez ids or Hugo symbols. If Hugo symbols are supplied, they will be converted to entrez ids using the get_entrez_id() function. If panel and genes are both supplied, genes from both arguments will be returned. If both are NULL (default), it will return gene results for all available genomic data for that sample.
panel: One or more panel IDs to query (e.g. 'IMPACT468'). If panel and genes are both supplied, genes from both arguments will be returned. If both are NULL (default), it will return gene results for all available genomic data for that sample.
add_hugo: Logical indicating whether HugoGeneSymbol should be added to your resulting data frame, if not already present in raw API results. Argument is TRUE by default. If FALSE, results will be returned as is (i.e. any existing Hugo Symbol columns in raw results will not be removed).
base_url: The database URL to query If NULL will default to URL set with set_cbioportal_db(<your_db>)

Value

A data frame of mutations (maf file format)

Examples

# \dontrun{
get_mutations_by_sample(sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
study_id = "acc_tcga",
base_url = "public")
#> The following parameters were used in query:
#> Study ID: "acc_tcga"
#> Molecular Profile ID: "acc_tcga_mutations"
#> Genes: "All available genes"
#> # A tibble: 173 × 28
#>    hugoGeneSymbol entrezGeneId uniqueSampleKey                  uniquePatientKey
#>    <chr>                 <int> <chr>                            <chr>           
#>  1 ZFPM1                161882 VENHQS1PUi1BNUoyLTAxOmFjY190Y2dh VENHQS1PUi1BNUo…
#>  2 ZFPM1                161882 VENHQS1PUi1BNUoyLTAxOmFjY190Y2dh VENHQS1PUi1BNUo…
#>  3 ZFPM1                161882 VENHQS1PUi1BNUoyLTAxOmFjY190Y2dh VENHQS1PUi1BNUo…
#>  4 ZFPM1                161882 VENHQS1PUi1BNUoyLTAxOmFjY190Y2dh VENHQS1PUi1BNUo…
#>  5 ZNF787               126208 VENHQS1PUi1BNUoyLTAxOmFjY190Y2dh VENHQS1PUi1BNUo…
#>  6 PODXL                  5420 VENHQS1PUi1BNUoyLTAxOmFjY190Y2dh VENHQS1PUi1BNUo…
#>  7 CCDC102A              92922 VENHQS1PUi1BNUoyLTAxOmFjY190Y2dh VENHQS1PUi1BNUo…
#>  8 TVP23C               201158 VENHQS1PUi1BNUoyLTAxOmFjY190Y2dh VENHQS1PUi1BNUo…
#>  9 RINL                 126432 VENHQS1PUi1BNUoyLTAxOmFjY190Y2dh VENHQS1PUi1BNUo…
#> 10 ZNF628                89887 VENHQS1PUi1BNUoyLTAxOmFjY190Y2dh VENHQS1PUi1BNUo…
#> # ℹ 163 more rows
#> # ℹ 24 more variables: molecularProfileId <chr>, sampleId <chr>,
#> #   patientId <chr>, studyId <chr>, center <chr>, mutationStatus <chr>,
#> #   validationStatus <chr>, tumorAltCount <int>, tumorRefCount <int>,
#> #   normalAltCount <int>, normalRefCount <int>, startPosition <int>,
#> #   endPosition <int>, referenceAllele <chr>, proteinChange <chr>,
#> #   mutationType <chr>, ncbiBuild <chr>, variantType <chr>, keyword <chr>, …
# }