Internal Function to Get Mutations/CNA/Fusion By Sample ID

Usage

.get_data_by_sample(
  sample_id = NULL,
  study_id = NULL,
  molecular_profile_id = NULL,
  sample_study_pairs = NULL,
  data_type = c("mutation", "cna", "fusion", "structural_variant", "segment"),
  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.
data_type: specify what type of data to return. Options aremutations, cna, fusion or structural_variant (same as fusion).
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 dataframe of mutations, CNAs or fusions.

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_data_by_sample(sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
 study_id = "acc_tcga", data_type = "mutation")
#> 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>, …

.get_data_by_sample(sample_id = c("DS-sig-010-P2"),
 molecular_profile_id = "blca_plasmacytoid_mskcc_2016_cna", data_type = "cna")
#> The following parameters were used in query:
#> Study ID: "blca_plasmacytoid_mskcc_2016"
#> Molecular Profile ID: "blca_plasmacytoid_mskcc_2016_cna"
#> Genes: "All available genes"
#> # A tibble: 2 × 9
#>   hugoGeneSymbol entrezGeneId uniqueSampleKey                   uniquePatientKey
#>   <chr>                 <int> <chr>                             <chr>           
#> 1 YAP1                  10413 RFMtc2lnLTAxMC1QMjpibGNhX3BsYXNt… RFMtc2lnLTAxMDp…
#> 2 CD79B                   974 RFMtc2lnLTAxMC1QMjpibGNhX3BsYXNt… RFMtc2lnLTAxMDp…
#> # ℹ 5 more variables: molecularProfileId <chr>, sampleId <chr>,
#> #   patientId <chr>, studyId <chr>, alteration <int>


.get_data_by_sample(sample_id = c("P-0002146-T01-IM3"),
 study_id = "blca_plasmacytoid_mskcc_2016", data_type = "fusion")
#> The following parameters were used in query:
#> Study ID: "blca_plasmacytoid_mskcc_2016"
#> Molecular Profile ID: "blca_plasmacytoid_mskcc_2016_structural_variants"
#> Genes: "All available genes"
#> # A tibble: 1 × 44
#>   uniqueSampleKey uniquePatientKey molecularProfileId sampleId patientId studyId
#>   <chr>           <chr>            <chr>              <chr>    <chr>     <chr>  
#> 1 UC0wMDAyMTQ2LV… UC0wMDAyMTQ2OmJ… blca_plasmacytoid… P-00021… P-0002146 blca_p…
#> # 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>, …

df_pairs <- data.frame(
"sample_id" = c("s_C_36924L_P001_d",
"s_C_03LNU8_P001_d"),
"study_id" = c("prad_msk_2019"))

.get_data_by_sample(sample_study_pairs = df_pairs, data_type = "mutation")
#> Joining with `by = join_by(study_id)`
#> The following parameters were used in query:
#> Study ID: "prad_msk_2019"
#> Molecular Profile ID: prad_msk_2019_mutations
#> Genes: "All available genes"
#> # A tibble: 1 × 28
#>   hugoGeneSymbol entrezGeneId uniqueSampleKey                   uniquePatientKey
#>   <chr>                 <int> <chr>                             <chr>           
#> 1 TP53                   7157 c19DXzAzTE5VOF9QMDAxX2Q6cHJhZF9t… cF9DXzAzTE5VODp…
#> # 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>,
#> #   chr <chr>, variantAllele <chr>, refseqMrnaId <chr>, …
.get_data_by_sample(sample_study_pairs = df_pairs, genes = 7157, data_type = "mutation")
#> Joining with `by = join_by(study_id)`
#> The following parameters were used in query:
#> Study ID: "prad_msk_2019"
#> Molecular Profile ID: prad_msk_2019_mutations
#> Genes: 7157
#> # A tibble: 1 × 28
#>   hugoGeneSymbol entrezGeneId uniqueSampleKey                   uniquePatientKey
#>   <chr>                 <int> <chr>                             <chr>           
#> 1 TP53                   7157 c19DXzAzTE5VOF9QMDAxX2Q6cHJhZF9t… cF9DXzAzTE5VODp…
#> # 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>,
#> #   chr <chr>, variantAllele <chr>, refseqMrnaId <chr>, …
.get_data_by_sample(sample_study_pairs = df_pairs, data_type = "cna")
#> Joining with `by = join_by(study_id)`
#> The following parameters were used in query:
#> Study ID: "prad_msk_2019"
#> Molecular Profile ID: prad_msk_2019_cna
#> Genes: "All available genes"
#> # 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>
.get_data_by_sample(sample_study_pairs = df_pairs, data_type = "fusion")
#> Joining with `by = join_by(study_id)`
#> The following parameters were used in query:
#> Study ID: "prad_msk_2019"
#> Molecular Profile ID: prad_msk_2019_structural_variants
#> Genes: "All available genes"
#> # A tibble: 0 × 0

df_pairs2 <- data.frame(
"sample_id" = c("P-0002146-T01-IM3", "s_C_CAUWT7_P001_d"),
 "study_id" = c("blca_plasmacytoid_mskcc_2016", "prad_msk_2019"))

.get_data_by_sample(sample_study_pairs = df_pairs2, data_type = "mutation")
#> Joining with `by = join_by(study_id)`
#> The following parameters were used in query:
#> Study ID: "blca_plasmacytoid_mskcc_2016" and "prad_msk_2019"
#> Molecular Profile ID: blca_plasmacytoid_mskcc_2016_mutations and
#> prad_msk_2019_mutations
#> Genes: "All available genes"
#> # A tibble: 7 × 28
#>   hugoGeneSymbol entrezGeneId uniqueSampleKey                   uniquePatientKey
#>   <chr>                 <int> <chr>                             <chr>           
#> 1 TP53                   7157 UC0wMDAyMTQ2LVQwMS1JTTM6YmxjYV9w… UC0wMDAyMTQ2OmJ…
#> 2 TP53                   7157 UC0wMDAyMTQ2LVQwMS1JTTM6YmxjYV9w… UC0wMDAyMTQ2OmJ…
#> 3 TERT                   7015 UC0wMDAyMTQ2LVQwMS1JTTM6YmxjYV9w… UC0wMDAyMTQ2OmJ…
#> 4 NOTCH4                 4855 UC0wMDAyMTQ2LVQwMS1JTTM6YmxjYV9w… UC0wMDAyMTQ2OmJ…
#> 5 BLM                     641 UC0wMDAyMTQ2LVQwMS1JTTM6YmxjYV9w… UC0wMDAyMTQ2OmJ…
#> 6 CDKN1A                 1026 UC0wMDAyMTQ2LVQwMS1JTTM6YmxjYV9w… UC0wMDAyMTQ2OmJ…
#> 7 RB1                    5925 UC0wMDAyMTQ2LVQwMS1JTTM6YmxjYV9w… UC0wMDAyMTQ2OmJ…
#> # 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>,
#> #   chr <chr>, variantAllele <chr>, refseqMrnaId <chr>, …
.get_data_by_sample(sample_study_pairs = df_pairs2, genes = 7157)
#> Joining with `by = join_by(study_id)`
#> The following parameters were used in query:
#> Study ID: "blca_plasmacytoid_mskcc_2016" and "prad_msk_2019"
#> Molecular Profile ID: blca_plasmacytoid_mskcc_2016_mutations and
#> prad_msk_2019_mutations
#> Genes: 7157
#> # A tibble: 2 × 28
#>   hugoGeneSymbol entrezGeneId uniqueSampleKey                   uniquePatientKey
#>   <chr>                 <int> <chr>                             <chr>           
#> 1 TP53                   7157 UC0wMDAyMTQ2LVQwMS1JTTM6YmxjYV9w… UC0wMDAyMTQ2OmJ…
#> 2 TP53                   7157 UC0wMDAyMTQ2LVQwMS1JTTM6YmxjYV9w… UC0wMDAyMTQ2OmJ…
#> # 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>,
#> #   chr <chr>, variantAllele <chr>, refseqMrnaId <chr>, …
.get_data_by_sample(sample_study_pairs = df_pairs2, data_type = "cna")
#> Joining with `by = join_by(study_id)`
#> The following parameters were used in query:
#> Study ID: "blca_plasmacytoid_mskcc_2016" and "prad_msk_2019"
#> Molecular Profile ID: blca_plasmacytoid_mskcc_2016_cna and prad_msk_2019_cna
#> Genes: "All available genes"
#> NULL
.get_data_by_sample(sample_study_pairs = df_pairs2, data_type = "fusion")
#> Joining with `by = join_by(study_id)`
#> The following parameters were used in query:
#> Study ID: "blca_plasmacytoid_mskcc_2016" and "prad_msk_2019"
#> Molecular Profile ID: blca_plasmacytoid_mskcc_2016_structural_variants and
#> prad_msk_2019_structural_variants
#> Genes: "All available genes"
#> # A tibble: 2 × 44
#>   uniqueSampleKey uniquePatientKey molecularProfileId sampleId patientId studyId
#>   <chr>           <chr>            <chr>              <chr>    <chr>     <chr>  
#> 1 UC0wMDAyMTQ2LV… UC0wMDAyMTQ2OmJ… blca_plasmacytoid… P-00021… P-0002146 blca_p…
#> 2 c19DX0NBVVdUN1… cF9DX0NBVVdUNzp… prad_msk_2019_str… s_C_CAU… p_C_CAUW… 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>, …
# }