Package 'cbioportalR' reference manual

Title:	Browse and Query Clinical and Genomic Data from cBioPortal
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.
Authors:	Karissa Whiting [aut, cre, cph]
Maintainer:	Karissa Whiting <[email protected]>
License:	MIT + file LICENSE
Version:	1.1.1
Built:	2024-11-21 23:21:47 UTC
Source:	CRAN

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)
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)

## 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)
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)

## 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)
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)

## 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)
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)
## 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)
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)

## 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)
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)

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

## 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)
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)

## 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()
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)

## 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
)
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)

## 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
)
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)
## 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
)
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)

## 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
)
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)
## 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
)
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)
## 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)
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)
## 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
)
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)
## 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
)
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)
## 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)
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)

## 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)
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)
## 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
)
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)
## 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
)
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)
## 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)
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)
## 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
)
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)
## 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
)
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)

## 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
)
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)

## 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)
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)

## 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
)
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)
## 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)
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)
## 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)
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)
## 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
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)
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)
## 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)

Connect to cBioPortal DB

Description

This function sets a base cBioPortal URL

Usage

set_cbioportal_db(db = NULL)
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)

## 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()
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)


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

## End(Not run)

Package 'cbioportalR'

Help Index

Get all available clinical attribute IDs for a study

Description

Usage

Arguments

Value

Examples

Get Available Gene Panels For a Database

Description

Usage

Arguments

Value

Examples

Get All Patient IDs in a Study

Description

Usage

Arguments

Value

Examples

Get Available Genomic Profiles For a Study or Database

Description

Usage

Arguments

Value

Examples

Get All Sample Lists Available For a Study

Description

Usage

Arguments

Value

Examples

Get All Sample IDs in a Study

Description

Usage

Arguments

Value

Examples

Get Metadata on All Available Studies in a Database

Description

Usage

Arguments

Value

Examples

Get Gene Name Alias for a Given Hugo Symbol

Description

Usage

Arguments

Value

Examples

Get cBioPortal Access Token

Description

Usage

Value

Author(s)

Examples

Get clinical data by attribute, study ID and patient ID

Description

Usage

Arguments

Value

Examples

Get clinical data by attribute, study ID and sample ID

Description

Usage

Arguments

Value

Examples

Get all available clinical data for a specified study

Description

Usage

Arguments

Value

Examples

Get CNA By Sample ID

Description

Usage

Arguments

Value

Examples