Title: Browse and Query Clinical and Genomic Data from cBioPortal
Version: 1.1.1
Description: Provides R users with direct access to genomic and clinical data from the 'cBioPortal' web resource via user-friendly functions that wrap 'cBioPortal's' existing API endpoints https://www.cbioportal.org/api/swagger-ui/index.html. Users can browse and query genomic data on mutations, copy number alterations and fusions, as well as data on tumor mutational burden ('TMB'), microsatellite instability status ('MSI'), 'FACETS' and select clinical data points (depending on the study). See https://www.cbioportal.org/ and Gao et al., (2013) <doi:10.1126/scisignal.2004088> for more information on the cBioPortal web resource.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: testthat (≥ 3.1.4), knitr (≥ 1.39), rmarkdown (≥ 2.14), covr (≥ 3.5.1), spelling
Depends: R (≥ 2.10)
Imports: httr (≥ 1.4.3), tibble (≥ 3.1.7), purrr (≥ 0.3.4), magrittr (≥ 2.0.3), rlang (≥ 1.0.3), glue (≥ 1.6.2), jsonlite (≥ 1.8.0), tidyr (≥ 1.2.0), dplyr (≥ 1.0.9), stringr (≥ 1.4.0), cli (≥ 3.3.0)
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://github.com/karissawhiting/cbioportalR, https://www.karissawhiting.com/cbioportalR/
BugReports: https://github.com/karissawhiting/cbioportalR/issues
Language: en-US
NeedsCompilation: no
Packaged: 2024-11-19 21:02:33 UTC; kwhiting
Author: Karissa Whiting ORCID iD [aut, cre, cph]
Maintainer: Karissa Whiting <karissa.whiting@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-20 09:30:02 UTC

cbioportalR: Browse and Query Clinical and Genomic Data from cBioPortal

Description

logo

Provides R users with direct access to genomic and clinical data from the 'cBioPortal' web resource via user-friendly functions that wrap 'cBioPortal's' existing API endpoints https://www.cbioportal.org/api/swagger-ui/index.html. Users can browse and query genomic data on mutations, copy number alterations and fusions, as well as data on tumor mutational burden ('TMB'), microsatellite instability status ('MSI'), 'FACETS' and select clinical data points (depending on the study). See https://www.cbioportal.org/ and Gao et al., (2013) doi:10.1126/scisignal.2004088 for more information on the cBioPortal web resource.

Author(s)

Maintainer: Karissa Whiting karissa.whiting@gmail.com (ORCID) [copyright holder]

See Also

Useful links:

Pipe operator

Description

See magrittr::%>% for details.

Arguments

lhs

A value or the magrittr placeholder.

rhs

A function call using the magrittr semantics.

Value

The result of calling rhs(lhs).

Get clinical data by attribute, study ID and sample ID

Description

Get clinical data by attribute, study ID and sample ID

Usage

.get_clinical_by_list_item(
  study_id = NULL,
  sample_id = NULL,
  clinical_attribute = NULL,
  base_url = NULL
)

Arguments

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_id

a vector of sample IDs (character)

clinical_attribute

one or more clinical attributes for your study. If none provided, will return all attributes available for studies

base_url

The database URL to query If NULL will default to URL set with ⁠set_cbioportal_db(<your_db>)⁠

Value

a dataframe of a specific clinical attribute

Examples

## Not run: 
.get_clinical_by_list_item(study_id = "acc_tcga", sample_id = "TCGA-OR-A5J2-01",
 clinical_attribute = "CANCER_TYPE", base_url = 'www.cbioportal.org/api')
 
## End(Not run)

Get clinical data by attribute, study ID and patient ID

Description

Get clinical data by attribute, study ID and patient ID

Usage

.get_clinical_pat_by_list_item(
  study_id = NULL,
  patient_id = NULL,
  clinical_attribute = NULL,
  base_url = NULL
)

Arguments

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

patient_id

a cBioPortal patient_id

clinical_attribute

one or more clinical attributes for your study. If none provided, will return all attributes available for studies

base_url

The database URL to query If NULL will default to URL set with ⁠set_cbioportal_db(<your_db>)⁠

Value

a dataframe of a specific clinical attribute

Examples

## Not run: 
.get_clinical_pat_by_list_item(study_id = "msk_impact_2017",
 patient_id = "P-0001453",
  base_url = 'www.cbioportal.org/api')
  
## End(Not run)

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

Description

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

## Not run: 
set_cbioportal_db("public")
.get_data_by_sample(sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
 study_id = "acc_tcga", data_type = "mutation")

.get_data_by_sample(sample_id = c("DS-sig-010-P2"),
 molecular_profile_id = "blca_plasmacytoid_mskcc_2016_cna", data_type = "cna")


.get_data_by_sample(sample_id = c("P-0002146-T01-IM3"),
 study_id = "blca_plasmacytoid_mskcc_2016", data_type = "fusion")

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")
.get_data_by_sample(sample_study_pairs = df_pairs, genes = 7157, data_type = "mutation")
.get_data_by_sample(sample_study_pairs = df_pairs, data_type = "cna")
.get_data_by_sample(sample_study_pairs = df_pairs, data_type = "fusion")

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")
.get_data_by_sample(sample_study_pairs = df_pairs2, genes = 7157)
.get_data_by_sample(sample_study_pairs = df_pairs2, data_type = "cna")
.get_data_by_sample(sample_study_pairs = df_pairs2, data_type = "fusion")

## End(Not run)

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

Description

Endpoints for retrieving mutation and cna data are structurally similar. This internal function allows you to pull data from either endpoint. It has logic for sensible default guesses at study_id and molecular_profile_id when those are NULL

Usage

.get_data_by_study(
  study_id = NULL,
  molecular_profile_id = NULL,
  data_type = c("mutation", "cna", "fusion", "structural_variant", "segment"),
  base_url = NULL,
  add_hugo = TRUE
)

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.

data_type

specify what type of data to return. Options aremutation, cna, fusion, orstructural_variant (same as fusion), and segment (copy number segmentation data)..

base_url

The database URL to query If NULL will default to URL set with ⁠set_cbioportal_db(<your_db>)⁠

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).

Value

a dataframe of mutations, CNAs or structural variants

Examples

## Not run: 
set_cbioportal_db("public")
.get_data_by_study(study_id = "prad_msk_2019", data_type = "cna")
.get_data_by_study(study_id = "prad_msk_2019", data_type = "mutation")
.get_data_by_study(study_id = "prad_msk_2019", data_type = "fusion")

.get_data_by_study(molecular_profile_id = "prad_msk_2019_cna", data_type = "cna")
.get_data_by_study(molecular_profile_id = "prad_msk_2019_mutations", data_type = "mutation")
.get_data_by_study(molecular_profile_id = "prad_msk_2019_structural_variants", data_type = "fusion")

## End(Not run)

Get all available clinical attribute IDs for a study

Description

Get all available clinical attribute IDs for a study

Usage

available_clinical_attributes(study_id = NULL, base_url = NULL)

Arguments

study_id

cbioportal study ID

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 available clinical attributes for that study

Examples

## Not run: 
available_clinical_attributes("acc_tcga", base_url = 'www.cbioportal.org/api')

## End(Not run)

Get Available Gene Panels For a Database

Description

Get Available Gene Panels For a Database

Usage

available_gene_panels(base_url = NULL)

Arguments

base_url

The database URL to query. If NULL will default to URL set with ⁠set_cbioportal_db(<your_db>)⁠

Value

a dataframe of metadata regarding each available panel

Examples

## Not run: 
set_cbioportal_db("public")
available_gene_panels()

## End(Not run)

Get All Patient IDs in a Study

Description

Get All Patient IDs in a Study

Usage

available_patients(study_id = NULL, base_url = NULL)

Arguments

study_id

A character string indicating which study ID should be searched. Only 1 study ID allowed.

base_url

The database URL to query If NULL will default to URL set with ⁠set_cbioportal_db(<your_db>)⁠

Value

A dataframe of patient_ids in a given study

Examples

## Not run: 
set_cbioportal_db("public")
available_samples(study_id = "acc_tcga")

## End(Not run)

Get Available Genomic Profiles For a Study or Database

Description

Get Available Genomic Profiles For a Study or Database

Usage

available_profiles(study_id = NULL, base_url = NULL)

Arguments

study_id

A character vector of length 1 indicating study_id. See get_studies() to see all available studies for your URL. If NULL, it will return all profiles for your current database url

base_url

The database URL to query. If NULL will default to URL set with ⁠set_cbioportal_db(<your_db>)⁠

Value

A dataframe of available genetic profiles and their profile ids

Examples

## Not run: 
set_cbioportal_db("public")
available_profiles()
available_profiles(study_id = "acc_tcga")

## End(Not run)

Get All Sample Lists Available For a Study

Description

Get All Sample Lists Available For a Study

Usage

available_sample_lists(study_id = NULL, base_url = NULL)

Arguments

study_id

A character string indicating which study ID should be searched. Only 1 study ID allowed.

base_url

The database URL to query If NULL will default to URL set with ⁠set_cbioportal_db(<your_db>)⁠

Value

A dataframe of patient_ids in a given study

Examples

## Not run: 
set_cbioportal_db("public")
available_sample_lists(study_id = "acc_tcga")

## End(Not run)

Get All Sample IDs in a Study

Description

Pulls all available sample IDs for a given study ID or sample list ID. Either a study ID or sample list ID must be passed. If both sample_list and study_id are not NULL, sample_list ID will be searched and study_id will be ignored.

Usage

available_samples(study_id = NULL, sample_list_id = NULL, base_url = NULL)

Arguments

study_id

A character string indicating which study ID should be searched. Only 1 study ID allowed.

sample_list_id

A character string indicating which sample list ID should be searched. Only 1 sample list ID allowed.

base_url

The database URL to query If NULL will default to URL set with ⁠set_cbioportal_db(<your_db>)⁠

Value

A dataframe of sample_ids in a given study

Examples

## Not run: 
set_cbioportal_db("public")
available_samples(study_id = "acc_tcga")
available_samples(sample_list_id = "acc_tcga_cna")

## End(Not run)

Get Metadata on All Available Studies in a Database

Description

Get Metadata on All Available Studies in a Database

Usage

available_studies(base_url = NULL)

Arguments

base_url

The database URL to query. If NULL will default to URL set with ⁠set_cbioportal_db(<your_db>)⁠

Value

A dataframe of available studies and their metadata

Examples

## Not run: 
set_cbioportal_db("public")
available_studies()

## End(Not run)

Core function to retrieve data from cBioPortal API.

Description

Core function to retrieve data from cBioPortal API.

Usage

cbp_api(
  url_path,
  method = NULL,
  token = get_cbioportal_token(),
  body = NULL,
  extra_box = FALSE,
  quiet = TRUE,
  base_url = NULL
)

Arguments

url_path

The url path for API call

method

Which API method to use. Must be "get" or "post". Default is "get".

token

Authentication token, if needed. Default is get_cbioportal_token()

body

Arguments passed to API call (e.g. sample ID or gene IDs)

extra_box

Some functions require an additional list() wrapping around body idk why

quiet

Returns queried URL. Default is TRUE

base_url

The database URL to query

Value

A parsed API response

Examples

## Not run: 
cbp_api(url_path = "genes/TP53", base_url = "public")

## End(Not run)

Get Gene Name Alias for a Given Hugo Symbol

Description

This function grabs known gene aliases for a given Hugo Symbol. You may notice that genes -alias pairs are not always consistent. For example get_alias("KMT2D") will return "MLL2" but get_alias("MLL2") will not return "KMT2D" This function relies on the existing cBioPortal API which controls this database of aliases. Therefore, this is a convenience function but you may want to consider a more carefully curated alias list like cbioportalR::impact_gene_info

Usage

get_alias(hugo_symbol = NULL, base_url = NULL)

Arguments

hugo_symbol

a hugo symbol for which to return aliases

base_url

The database URL to query

Value

A character string with all aliases

Examples

## Not run: 

get_alias(hugo_symbol = "FGFR3", base_url = 'www.cbioportal.org/api')
get_alias(hugo_symbol = c("FGFR3", "TP53"), base_url = 'www.cbioportal.org/api')

## End(Not run)

Get cBioPortal Access Token

Description

Convenience function that retrieves cBioPortal token System Environment variable "CBIOPORTAL_TOKEN"

Usage

get_cbioportal_token()

Value

Returns a string with cBioPortal token if successfully authenticated, or a warning that token could not be found.

Author(s)

Karissa Whiting, Daniel D. Sjoberg

Examples

## Not run: 
get_cbioportal_token()

## End(Not run)

Get clinical data by attribute, study ID and patient ID

Description

Get clinical data by attribute, study ID and patient ID

Usage

get_clinical_by_patient(
  study_id = NULL,
  patient_id = NULL,
  patient_study_pairs = NULL,
  clinical_attribute = NULL,
  base_url = NULL
)

Arguments

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

patient_id

a cBioPortal patient_id

patient_study_pairs

A dataframe with columns: patient_id, study_id. Variations in capitalization of column names are accepted. This can be used in place of patient_id, study_id, arguments above if you need to pull samples from several different studies at once. If passed, this will take overwrite patient_id and study_id if they are also passed.

clinical_attribute

one or more clinical attributes for your study. If none provided, will return all attributes available for studies

base_url

The database URL to query If NULL will default to URL set with ⁠set_cbioportal_db(<your_db>)⁠

Value

a dataframe of a specific clinical attribute

Examples

## Not run: 

ex <- tibble::tribble(
~patientID, ~study_id,
"P-0001453", "blca_nmibc_2017",
"P-0002166", "blca_nmibc_2017",
"P-0003238", "blca_nmibc_2017",
"P-0000004", "msk_impact_2017",
"P-0000023", "msk_impact_2017")

x <- get_clinical_by_patient(patient_study_pairs = ex,
 clinical_attribute = NULL, base_url = 'www.cbioportal.org/api')
 
## End(Not run)

Get clinical data by attribute, study ID and sample ID

Description

Get clinical data by attribute, study ID and sample ID

Usage

get_clinical_by_sample(
  study_id = NULL,
  sample_id = NULL,
  sample_study_pairs = NULL,
  clinical_attribute = NULL,
  base_url = NULL
)

Arguments

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_id

a vector of sample IDs (character)

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.

clinical_attribute

one or more clinical attributes for your study. If none provided, will return all attributes available for studies

base_url

The database URL to query If NULL will default to URL set with ⁠set_cbioportal_db(<your_db>)⁠

Value

a dataframe of a specific clinical attribute

Examples

## Not run: 
get_clinical_by_sample(study_id = "acc_tcga", sample_id = "TCGA-OR-A5J2-01",
 clinical_attribute = "CANCER_TYPE", base_url = 'www.cbioportal.org/api')

ex <- tibble::tribble(
~sample_id, ~study_id,
"P-0001453-T01-IM3", "blca_nmibc_2017",
"P-0002166-T01-IM3", "blca_nmibc_2017",
"P-0003238-T01-IM5", "blca_nmibc_2017",
"P-0000004-T01-IM3", "msk_impact_2017",
"P-0000023-T01-IM3", "msk_impact_2017")

x <- get_clinical_by_sample(sample_study_pairs = ex,
 clinical_attribute = NULL, base_url = 'www.cbioportal.org/api')
 
## End(Not run)

Get all available clinical data for a specified study

Description

Returns all sample-level and patient-level clinical data for a given study

Usage

get_clinical_by_study(
  study_id = NULL,
  clinical_attribute = NULL,
  base_url = NULL
)

Arguments

study_id

study ID

clinical_attribute

one or more clinical attributes for your study. If none provided, will return all attributes available for that study (⁠available_clinical_attributes(<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 all available clinical attributes and their values

Examples

## Not run: 
get_clinical_by_study(study_id = "acc_tcga",
 clinical_attribute = "CANCER_TYPE", base_url = 'www.cbioportal.org/api')

get_clinical_by_study(study_id = "acc_tcga", base_url = 'www.cbioportal.org/api')

## End(Not run)

Get CNA By Sample ID

Description

Get CNA By Sample ID

Usage

get_cna_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 CNAs

Examples

## Not run: 
set_cbioportal_db("public")
get_cna_by_sample(sample_id = c("s_C_36924L_P001_d"),
                 study_id = "prad_msk_2019")

## End(Not run)

Get CNA By Study

Description

Get CNA By Study

Usage

get_cna_by_study(
  study_id = NULL,
  molecular_profile_id = NULL,
  add_hugo = TRUE,
  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.

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 CNAs

Examples

## Not run: 
get_cna_by_study(study_id = "prad_msk_2019")
get_cna_by_study(molecular_profile_id = "prad_msk_2019_cna")

## End(Not run)

Get Entrez Gene ID for a given set of Hugo Symbols

Description

Get Entrez Gene ID for a given set of Hugo Symbols

Usage

get_entrez_id(hugo_symbol = NULL, base_url = NULL)

Arguments

hugo_symbol

a character vector of Hugo Symbols

base_url

The database URL to query

Value

A dataframe with Entrez Gene IDs and Hugo Symbols

Examples

## Not run: 
get_entrez_id(hugo_symbol = "TAP1", base_url = 'www.cbioportal.org/api')
get_entrez_id(hugo_symbol = c("FGFR1", "TP53") , base_url = 'www.cbioportal.org/api')

## End(Not run)

Get Fusions By Sample ID

Description

Get Fusions By Sample ID

Usage

get_fusions_by_sample(
  sample_id = NULL,
  study_id = NULL,
  molecular_profile_id = NULL,
  sample_study_pairs = NULL,
  genes = NULL,
  panel = NULL,
  base_url = NULL
)

get_structural_variants_by_sample(
  sample_id = NULL,
  study_id = NULL,
  molecular_profile_id = NULL,
  sample_study_pairs = NULL,
  genes = NULL,
  panel = 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

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.

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 Fusions

Examples

## Not run: 
set_cbioportal_db("public")

#' # These return the same results
get_fusions_by_sample(sample_id = c("s_C_CAUWT7_P001_d"),
                 study_id = "prad_msk_2019")
get_structural_variants_by_sample(sample_id = c("s_C_CAUWT7_P001_d"),
                 study_id = "prad_msk_2019")
                 
## End(Not run)

Get Fusions By Study

Description

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

## Not run: 
# These return the same results
get_fusions_by_study(molecular_profile_id = "prad_msk_2019_structural_variants")

get_structural_variants_by_study(molecular_profile_id =
       "prad_msk_2019_structural_variants")
       
## End(Not run)

Retrieve Genes Included For a Specified Panel ID

Description

Retrieve Genes Included For a Specified Panel ID

Usage

get_gene_panel(panel_id = NULL, base_url = NULL)

Arguments

panel_id

name of panel. See available_gene_panels() to get panel 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 genes in a specified panel

Examples

## Not run: 
get_gene_panel(panel_id = "IMPACT468", base_url = 'www.cbioportal.org/api')

## End(Not run)

Get A List of Genes for a Specified Database

Description

Get A List of Genes for a Specified Database

Usage

get_genes(base_url = NULL)

Arguments

base_url

The database URL to query If NULL will default to URL set with ⁠set_cbioportal_db(<your_db>)⁠

Value

A dataframe of gene ids, hugo symbols, and gene types

Examples

## Not run: 
get_genes(base_url = 'www.cbioportal.org/api')

## End(Not run)

Get All Genomic Information By Sample IDs

Description

Get All Genomic Information By Sample IDs

Usage

get_genetics_by_sample(
  sample_id = NULL,
  study_id = NULL,
  sample_study_pairs = NULL,
  genes = NULL,
  panel = NULL,
  add_hugo = TRUE,
  base_url = NULL,
  return_segments = FALSE
)

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.

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>)⁠

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

## Not run: 
get_genetics_by_sample(sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
 study_id = "acc_tcga",
 return_segments = TRUE)

## End(Not run)

Get All Genomic Information By Study

Description

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

## Not run: 
get_genetics_by_study(study_id = "prad_msk_2019")

## End(Not run)

Get Hugo Symbol for a given set of Entrez IDs

Description

Get Hugo Symbol for a given set of Entrez IDs

Usage

get_hugo_symbol(entrez_id = NULL, base_url = NULL)

Arguments

entrez_id

a character or numeric vector of Entrez gene IDs

base_url

The database URL to query

Value

A dataframe with Entrez Gene IDs and Hugo Symbols

Examples

## Not run: 
get_hugo_symbol(entrez_id = 2261, base_url = 'www.cbioportal.org/api')
get_hugo_symbol(entrez_id = c(2261, 7157) , base_url = 'www.cbioportal.org/api')

## End(Not run)

Get Mutations By Sample ID

Description

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

## Not run: 
get_mutations_by_sample(sample_id = c("TCGA-OR-A5J2-01","TCGA-OR-A5J6-01"),
study_id = "acc_tcga",
base_url = "public")

## End(Not run)

Get Mutations By Study ID

Description

Get Mutations By Study ID

Usage

get_mutations_by_study(
  study_id = NULL,
  molecular_profile_id = NULL,
  add_hugo = TRUE,
  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.

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 (maf file format)

Examples

## Not run: 
get_mutations_by_study(study_id = "prad_msk_2019")
get_mutations_by_study(molecular_profile_id = "prad_msk_2019_mutations")

## End(Not run)

Get Gene Panel by study ID and sample ID

Description

Get Gene Panel by study ID and sample ID

Usage

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

Arguments

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_id

a vector of sample IDs (character)

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 a specific clinical attribute

Examples

## Not run: 
get_panel_by_sample(study_id = "blca_plasmacytoid_mskcc_2016",
 sample_id = "DS-sig-010-P2",
 base_url = 'www.cbioportal.org/api')
 
## End(Not run)

Get sample IDs for a given set of patient IDs

Description

Get sample IDs for a given set of patient IDs

Usage

get_samples_by_patient(patient_id = NULL, study_id = NULL, base_url = NULL)

Arguments

patient_id

A character string of sample IDs to query

study_id

A character string indicating which study ID should be searched. Only 1 study allowed. If NULL, we will guess a default study ID based on your database URL.

base_url

The database URL to query If NULL will default to URL set with ⁠set_cbioportal_db(<your_db>)⁠

Value

A dataframe of patient IDs and corresponding sample IDs. If patient has multiple samples, there will be multiple rows per patient.

Examples

## Not run: 
get_samples_by_patient(patient_id = c("P-0000034", "P-0000036"))

## End(Not run)

Get Copy Number Segmentation Data By Sample ID

Description

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

## Not run: 
set_cbioportal_db("public")

get_segments_by_sample(sample_id = c("s_C_CAUWT7_P001_d"),
                 study_id = "prad_msk_2019")
                 
## End(Not run)

Get Copy Number Segmentation Data By Study

Description

Get Copy Number Segmentation Data By Study

Usage

get_segments_by_study(study_id = NULL, add_hugo = TRUE, base_url = NULL)

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>)⁠

Value

A dataframe of CNA segments

Examples

## Not run: 
get_segments_by_study(study_id = "prad_msk_2019")
get_segments_by_study(molecular_profile_id = "prad_msk_2019_cna")

## End(Not run)

Get Metadata on All Available Studies in Database or a Specified Study

Description

Get Metadata on All Available Studies in Database or a Specified Study

Usage

get_study_info(study_id = NULL, base_url = NULL)

Arguments

study_id

one or more study IDs (see available_studies() to lookup IDs)

base_url

The database URL to query. If NULL will default to URL set with ⁠set_cbioportal_db(<your_db>)⁠

Value

A dataframe of study metadata

Examples

## Not run: 
set_cbioportal_db("public")
get_study_info("acc_tcga")

## End(Not run)

IMPACT Gene Meta Data

Description

Dataframe labeling all genes included in IMPACT panels along with their corresponding platform ID and Entrez ID.

Usage

impact_gene_info

Format

A data frame with 470 genes

hugo_symbol

Factor w/ 574 levels, Column containing all HUGO symbols genes included in IMPACT

entrez_id

Integer, contains all Entrez IDs for genes included in IMPACT

platform_341

Character, indicates whether each gene was included in IMPACT platform 341. Options are included and ⁠not included⁠

platform_410

Character, indicates whether each gene was included in IMPACT platform 410. Options are included and ⁠not included⁠

platform_468

Character, indicates whether each gene was included in IMPACT platform 468. Options are included and ⁠not included⁠

alias

A nested dataframe of aliases for each gene and corresponding entrez gene ids for aliases if they exist

Source

http://www.cbioportal.org/

Lookup all available information on what studies a sample ID or patient ID belongs to

Description

This is a general look up function that can take a study ID or patient ID and return what samples exist across entire cBioPortal website (depends on your base URL) that match that ID. It will return which studies include that sample or patient.

Usage

lookup_id(lookup_id = NULL, base_url = NULL)

Arguments

lookup_id

a sample ID or patient ID

base_url

The database URL to query If NULL will default to URL set with ⁠set_cbioportal_db(<your_db>)⁠

Details

This can also be useful to see all samples a particular patient has available across all studies on cBioPortal (see also get_samples_by_patient()).

Value

A dataframe of general info for sample of patient IDs given

Examples

## Not run: 
lookup_id <- c("P-0001453-T01-IM3", "P-0000004-T01-IM3", "TCGA-OR-A5JA")
x <- lookup_id(lookup_id = lookup_id,  base_url = 'www.cbioportal.org/api')
x
 
## End(Not run)

Default value for NULL.

Description

Default value for NULL.

Connect to cBioPortal DB

Description

This function sets a base cBioPortal URL

Usage

set_cbioportal_db(db = NULL)

Arguments

db

The database URL to use as base URL for calls, or "public" for https://www.cbioportal.org/

Value

No return value, called for side effects. Will display an alert notifying if the user has successfully authenticated to cBioPortal.

Author(s)

Karissa Whiting, Daniel D. Sjoberg

Examples

## Not run: 
set_cbioportal_db(db = "public")

## End(Not run)

Test the Database Connection Anytime During your R Session

Description

Helps troubleshoot API issues during an R session

Usage

test_cbioportal_db()

Value

No return value, called for side effects. Will display an alert notifying if the user has successfully authenticated to cBioPortal

Author(s)

Karissa Whiting, Daniel D. Sjoberg

Examples

## Not run: 
set_cbioportal_db("public")
test_cbioportal_db()

## End(Not run)