Get All Genomic Information By Study

Get All Genomic Information By Study

Usage

get_genetics_by_study(
  study_id = NULL,
  add_hugo = TRUE,
  base_url = NULL,
  return_segments = FALSE
)

Arguments

study_id

A study ID to query mutations. If NULL, guesses study ID based on molecular_profile_id.

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>)

return_segments

Default is FALSE where copy number segmentation data won't be returned in addition to the mutation, cna and structural variant data. TRUE will return any available segmentation data with results.

Value

A list of mutations, cna and structural variants (including fusions), if available. Will also return copy number segmentation data if return_segments = TRUE.

Examples

# \dontrun{
get_genetics_by_study(study_id = "prad_msk_2019")
#> ℹ Returning all data for the "prad_msk_2019_mutations" molecular profile in the "prad_msk_2019" study
#> ℹ Returning all data for the "prad_msk_2019_cna" molecular profile in the "prad_msk_2019" study
#> ℹ Returning all data for the "prad_msk_2019_structural_variants" molecular profile in the "prad_msk_2019" study
#> $mutation
#> # A tibble: 26 × 28
#>    hugoGeneSymbol entrezGeneId uniqueSampleKey                  uniquePatientKey
#>    <chr>                 <int> <chr>                            <chr>           
#>  1 ZFHX3                   463 c19DX004WDQyVF9QMDAyX2Q6cHJhZF9… cF9DX004WDQyVDp…
#>  2 ZFHX3                   463 c19DX004WDQyVF9QMDAyX2Q6cHJhZF9… cF9DX004WDQyVDp…
#>  3 ATR                     545 c19DX004WDQyVF9QMDAyX2Q6cHJhZF9… cF9DX004WDQyVDp…
#>  4 BCL2                    596 c19DX004WDQyVF9QMDAyX2Q6cHJhZF9… cF9DX004WDQyVDp…
#>  5 ETV1                   2115 c19DX1A4SzNUUl9QMDAxX2Q6cHJhZF9… cF9DX1A4SzNUUjp…
#>  6 ETV1                   2115 c19DX1A4SzNUUl9QMDAzX2Q6cHJhZF9… cF9DX1A4SzNUUjp…
#>  7 FAT1                   2195 c19DX004WDQyVF9QMDAyX2Q6cHJhZF9… cF9DX004WDQyVDp…
#>  8 MSH6                   2956 c19DX1A4SzNUUl9QMDAyX2Q6cHJhZF9… cF9DX1A4SzNUUjp…
#>  9 MSH6                   2956 c19DX1A4SzNUUl9QMDAzX2Q6cHJhZF9… cF9DX1A4SzNUUjp…
#> 10 FOXA1                  3169 c19DX0UwS0pGSl9QMDAyX2Q6cHJhZF9… cF9DX0UwS0pGSjp…
#> # ℹ 16 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>, …
#> 
#> $cna
#> # A tibble: 1 × 9
#>   hugoGeneSymbol entrezGeneId uniqueSampleKey                   uniquePatientKey
#>   <chr>                 <int> <chr>                             <chr>           
#> 1 PTEN                   5728 c19DXzM2OTI0TF9QMDAxX2Q6cHJhZF9t… cF9DXzM2OTI0TDp…
#> # ℹ 5 more variables: molecularProfileId <chr>, sampleId <chr>,
#> #   patientId <chr>, studyId <chr>, alteration <int>
#> 
#> $structural_variant
#> # 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>, …
#> 
# }