### Install cbioportalR Package

Source: https://github.com/karissawhiting/cbioportalr/blob/main/README.md

Provides R code to install the cbioportalR package from CRAN and the development version from GitHub.

```r
install.packages("cbioportalR")
```

```r
remotes::install_github("karissawhiting/cbioportalR")
```

--------------------------------

### Get Panel by Sample

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Returns the gene panel used for specific samples.

```APIDOC
## GET /api/panel/by_sample

### Description
Returns the gene panel used for specific samples.

### Method
GET

### Endpoint
/api/panel/by_sample

### Parameters
#### Query Parameters
- **sample_id** (string) - Required - The ID of the sample.
- **study_id** (string) - Required - The ID of the study.

### Request Example
```json
{
  "sample_id": "DS-sig-010-P2",
  "study_id": "blca_plasmacytoid_mskcc_2016"
}
```

### Response
#### Success Response (200)
- **data** (object) - Information about the gene panel used for the sample.

#### Response Example
```json
{
  "data": {
    "sampleId": "DS-sig-010-P2",
    "studyId": "blca_plasmacytoid_mskcc_2016",
    "genePanel": "IMPACT341"
  }
}
```
```

--------------------------------

### Get Segmentation Data by Sample

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Retrieves segmentation data for specific samples within a study.

```APIDOC
## GET /api/segments/by_sample

### Description
Retrieves segmentation data for specific samples.

### Method
GET

### Endpoint
/api/segments/by_sample

### Parameters
#### Query Parameters
- **sample_id** (string array) - Required - A list of sample IDs to retrieve data for.
- **study_id** (string) - Required - The ID of the study to query.

### Request Example
```json
{
  "sample_id": ["s_C_CAUWT7_P001_d"],
  "study_id": "prad_msk_2019"
}
```

### Response
#### Success Response (200)
- **data** (object) - Segmentation data for the requested samples.

#### Response Example
```json
{
  "data": { ... segmentation data ... }
}
```
```

--------------------------------

### Get Clinical Data by Sample

Source: https://github.com/karissawhiting/cbioportalr/blob/main/README.md

Retrieves clinical data for specific samples within a study.

```APIDOC
## GET /api/samples/clinical_data

### Description
Retrieves clinical data for specific samples within a study.

### Method
GET

### Endpoint
/api/samples/clinical_data

### Parameters
#### Query Parameters
- **sample_id** (string) - Required - The ID of the sample(s) to retrieve clinical data for.
- **study_id** (string) - Required - The ID of the study.
- **clinical_attribute** (string) - Optional - Filters the data to a specific clinical attribute.

### Request Example
```r
samples <- c("SAMPLE1", "SAMPLE2")
clinical_data <- get_clinical_by_sample(sample_id = samples, study_id = "acc_tcga")
```

### Response
#### Success Response (200)
- **data** (list) - A list containing clinical data for the specified samples.

#### Response Example
```json
[
  {
    "uniqueSampleKey": "VENHQS1PUi1BNUoxLTAxOmFjY190Y2dh",
    "uniquePatientKey": "VENHQS1PUi1BNUoxLTAxOmFjY190Y2dh",
    "sampleId": "TCGA-OR-A5K5-01A",
    "patientId": "TCGA-OR-A5K5",
    "studyId": "acc_tcga",
    "clinicalAttributeId": "AGE",
    "value": "58"
  }
]
```
```

--------------------------------

### Get Mutations by Sample

Source: https://github.com/karissawhiting/cbioportalr/blob/main/README.md

Retrieves mutation data for specified samples within a given study. Demonstrates how to handle cases where no results are returned and how to correctly specify the study ID.

```APIDOC
## GET /api/mutations/samples

### Description
Retrieves mutation data for specified samples within a given study. Handles cases where no results are returned and demonstrates correct study ID specification.

### Method
GET

### Endpoint
/api/mutations/samples

### Parameters
#### Query Parameters
- **sample_id** (string) - Required - The ID of the sample(s) to retrieve mutations for.
- **study_id** (string) - Required - The ID of the study.

### Request Example
```r
samples <- c("SAMPLE1", "SAMPLE2")
mutations <- get_mutations_by_sample(sample_id = samples, study_id = "acc_tcga")
```

### Response
#### Success Response (200)
- **mutations** (list) - A list of mutations associated with the provided samples and study.

#### Response Example
```json
[
  {
    "hugoGeneSymbol": "KRT8",
    "entrezGeneId": 3856,
    "uniqueSampleKey": "VENHQS1PUi1BNUoxLTAxOmFjY190Y2dh",
    "uniquePatientKey": "VENHQS1PUi1BNUoxLTAxOmFjY190Y2dh",
    "sampleId": "TCGA-OR-A5K5-01A",
    "patientId": "TCGA-OR-A5K5",
    "studyId": "acc_tcga",
    "molecularProfileId": "acc_tcga_mutations",
    "mutationStatus": "Mutated",
    "validationStatus": "Valid",
    "tumorAltCount": 10,
    "tumorRefCount": 50,
    "normalAltCount": 0,
    "normalRefCount": 0,
    "startPosition": 12345,
    "endPosition": 12345,
    "referenceAllele": "A",
    "variantAllele": "T",
    "mutationType": "Missense_Mutation",
    "proteinChange": "p.Val123Ala",
    "ncbiBuild": "GRCh38",
    "variantType": "SNP",
    "chr": "1",
    "keyword": "Mutation",
    "center": "Broad",
    "refseqMrnaId": "NM_002247.3"
  }
]
```
```

--------------------------------

### Get Samples by Patient

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Returns all sample IDs associated with a given patient ID, useful when patients have multiple samples.

```APIDOC
## GET /api/samples/by_patient

### Description
Returns all sample IDs associated with a given patient ID.

### Method
GET

### Endpoint
/api/samples/by_patient

### Parameters
#### Query Parameters
- **patient_id** (string array) - Required - A list of patient IDs.
- **study_id** (string) - Required - The ID of the study.

### Request Example
```json
{
  "patient_id": ["P-0000034", "P-0000036"],
  "study_id": "msk_impact_2017"
}
```

### Response
#### Success Response (200)
- **data** (object) - A list of samples associated with the patient IDs.

#### Response Example
```json
{
  "data": [
    { "patientId": "P-0000034", "sampleId": "P-0000034-T01-IM3", "sampleType": "Primary", "studyId": "msk_impact_2017" },
    { "patientId": "P-0000034", "sampleId": "P-0000034-T02-IM5", "sampleType": "Metastasis", "studyId": "msk_impact_2017" }
  ]
}
```
```

--------------------------------

### Get Clinical Data by Study

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

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

```APIDOC
## GET /api/clinical/by_study

### Description
Retrieves all sample-level and patient-level clinical data for a study.

### Method
GET

### Endpoint
/api/clinical/by_study

### Parameters
#### Query Parameters
- **study_id** (string) - Required - The ID of the study.
- **clinical_attribute** (string array) - Optional - A list of specific clinical attributes to retrieve.

### Request Example
```json
{
  "study_id": "acc_tcga"
}
```

### Response
#### Success Response (200)
- **sample_level_data** (object) - Sample-level clinical data.
- **patient_level_data** (object) - Patient-level clinical data.

#### Response Example
```json
{
  "sample_level_data": { ... },
  "patient_level_data": { ... }
}
```
```

--------------------------------

### Configure cBioPortal Database Connection

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Sets the base URL for the cBioPortal API connection. This function must be called at the start of an R session to establish connectivity.

```R
library(cbioportalR)
set_cbioportal_db(db = "public")
set_cbioportal_db(db = "cbioportal.mskcc.org")
set_cbioportal_db(db = "https://www.cbioportal.org")
```

--------------------------------

### Get Detailed Study Information

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Fetches comprehensive metadata for a specific study, including sample counts and reference genome information.

```R
study_info <- get_study_info("acc_tcga")
t(study_info)
```

--------------------------------

### Get Clinical Data by Study

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Retrieves all sample-level and patient-level clinical data for a specified study. It can also filter for specific clinical attributes.

```r
# Get all clinical data for a study
clinical_data <- get_clinical_by_study(study_id = "acc_tcga")

clinical_data

# Get specific clinical attributes only
age_sex <- get_clinical_by_study(
  study_id = "acc_tcga",
  clinical_attribute = c("AGE", "SEX")
)
```

--------------------------------

### Get Clinical Data by Sample

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Retrieves sample-level clinical data for specific samples, optionally filtering by clinical attributes or querying across multiple studies.

```APIDOC
## GET /api/clinical/by_sample

### Description
Retrieves sample-level clinical data for specific samples.

### Method
GET

### Endpoint
/api/clinical/by_sample

### Parameters
#### Query Parameters
- **sample_id** (string array) - Required (if `sample_study_pairs` is not provided) - A list of sample IDs.
- **study_id** (string) - Required (if `sample_study_pairs` is not provided) - The ID of the study.
- **sample_study_pairs** (object array) - Required (if `sample_id` and `study_id` are not provided) - An array of objects, where each object contains `sample_id` and `study_id`.
- **clinical_attribute** (string array) - Optional - A list of specific clinical attributes to retrieve.

### Request Example
```json
{
  "sample_id": ["TCGA-OR-A5J2-01", "TCGA-OR-A5J6-01"],
  "study_id": "acc_tcga",
  "clinical_attribute": ["CANCER_TYPE", "MUTATION_COUNT", "FRACTION_GENOME_ALTERED"]
}
```

### Response
#### Success Response (200)
- **data** (object) - Sample-level clinical data.

#### Response Example
```json
{
  "data": { ... clinical data ... }
}
```
```

--------------------------------

### GET /genes/aliases

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Retrieves gene aliases for specified HUGO symbols.

```APIDOC
## GET /genes/aliases

### Description
Retrieves a list of aliases for the provided HUGO gene symbols.

### Method
GET

### Parameters
#### Query Parameters
- **hugo_symbol** (array) - Required - A vector of HUGO gene symbols to query.

### Request Example
get_alias(hugo_symbol = c("FGFR3", "TP53"))

### Response
#### Success Response (200)
- **hugo_symbol** (string) - The queried symbol
- **alias** (string) - The associated alias

#### Response Example
[{"hugo_symbol": "FGFR3", "alias": "ACH"}, {"hugo_symbol": "TP53", "alias": "p53"}]
```

--------------------------------

### Get Genes

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Returns a list of all genes available in the cBioPortal database with their Entrez IDs and Hugo symbols.

```APIDOC
## GET /api/genes

### Description
Returns a list of all genes available in the cBioPortal database.

### Method
GET

### Endpoint
/api/genes

### Parameters
None

### Request Example
```json
{}
```

### Response
#### Success Response (200)
- **data** (array) - A list of gene objects, each containing `entrezGeneId`, `hugoGeneSymbol`, and `type`.

#### Response Example
```json
{
  "data": [
    { "entrezGeneId": 1, "hugoGeneSymbol": "A1BG", "type": "protein-coding" },
    { "entrezGeneId": 2, "hugoGeneSymbol": "A2M", "type": "protein-coding" }
  ]
}
```
```

--------------------------------

### GET /get_mutations_by_sample

Source: https://github.com/karissawhiting/cbioportalr/blob/main/README.md

Retrieves mutation data for specific samples within a cBioPortal study. This endpoint requires sample identifiers and associated study identifiers to filter genomic data effectively.

```APIDOC
## GET /get_mutations_by_sample

### Description
Retrieves mutation data for a list of samples. If study_id is not provided, the system defaults to the public IMPACT database (msk_impact_2017).

### Method
GET

### Endpoint
/get_mutations_by_sample

### Parameters
#### Query Parameters
- **sample_id** (array) - Required - A list of sample identifiers to query.
- **study_id** (string) - Optional - The study identifier where the samples are housed. Defaults to 'msk_impact_2017'.
- **molecular_profile_id** (string) - Optional - The specific molecular profile to query.

### Request Example
{
  "sample_id": ["TCGA-OR-A5J1-01"],
  "study_id": "acc_tcga"
}

### Response
#### Success Response (200)
- **data** (table) - A dataframe containing gene symbols, Entrez IDs, molecular profile IDs, sample IDs, patient IDs, study IDs, and alteration counts.

#### Response Example
{
  "gene": "FRS2",
  "entrez_gene_id": 10818,
  "sampleId": "TCGA-OR-A5J1-01",
  "alteration": 1
}
```

--------------------------------

### GET /gene-panels/{panel_id}

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Retrieves detailed information about genes included in a specific gene panel.

```APIDOC
## GET /gene-panels/{panel_id}

### Description
Returns detailed information about genes included in a specific gene panel or multiple panels.

### Method
GET

### Parameters
#### Path Parameters
- **panel_id** (string/array) - Required - The ID or list of IDs of the gene panels.

### Request Example
get_gene_panel(panel_id = "IMPACT468")

### Response
#### Success Response (200)
- **genePanelId** (string) - The panel identifier
- **entrezGeneId** (integer) - The Entrez ID of the gene
- **hugoGeneSymbol** (string) - The HUGO symbol
- **description** (string) - Panel description

#### Response Example
[{"genePanelId": "IMPACT468", "entrezGeneId": 25, "hugoGeneSymbol": "ABL1", "description": "MSK-IMPACT"}]
```

--------------------------------

### Get Gene Aliases

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Returns known gene aliases for a given Hugo Symbol.

```APIDOC
## GET /api/genes/alias

### Description
Returns known gene aliases for a given Hugo Symbol.

### Method
GET

### Endpoint
/api/genes/alias

### Parameters
#### Query Parameters
- **hugo_symbol** (string) - Required - The Hugo Symbol for which to retrieve aliases.

### Request Example
```json
{
  "hugo_symbol": "FGFR1"
}
```

### Response
#### Success Response (200)
- **data** (array) - A list of gene aliases for the given Hugo Symbol.

#### Response Example
```json
{
  "data": ["CDK5RAP2", "FLG", "FLJ107583", "FLJ11057", "FLJ11124", "FLJ11210", "FLJ11287", "FLJ11307", "FLJ11347", "FLJ11423", "FLJ11535", "FLJ11668", "FLJ11731", "FLJ11840", "FLJ11934", "FLJ12171", "FLJ12267", "FLJ12300", "FLJ12314", "FLJ12320", "FLJ12340", "FLJ12377", "FLJ12411", "FLJ12431", "FLJ12445", "FLJ12476", "FLJ12500", "FLJ12509", "FLJ12510", "FLJ12513", "FLJ12515", "FLJ12517", "FLJ12519", "FLJ12521", "FLJ12523", "FLJ12525", "FLJ12527", "FLJ12529", "FLJ12531", "FLJ12533", "FLJ12535", "FLJ12537", "FLJ12539", "FLJ12541", "FLJ12543", "FLJ12545", "FLJ12547", "FLJ12549", "FLJ12551", "FLJ12553", "FLJ12555", "FLJ12557", "FLJ12559", "FLJ12561", "FLJ12563", "FLJ12565", "FLJ12567", "FLJ12569", "FLJ12571", "FLJ12573", "FLJ12575", "FLJ12577", "FLJ12579", "FLJ12581", "FLJ12583", "FLJ12585", "FLJ12587", "FLJ12589", "FLJ12591", "FLJ12593", "FLJ12595", "FLJ12597", "FLJ12599", "FLJ12601", "FLJ12603", "FLJ12605", "FLJ12607", "FLJ12609", "FLJ12611", "FLJ12613", "FLJ12615", "FLJ12617", "FLJ12619", "FLJ12621", "FLJ12623", "FLJ12625", "FLJ12627", "FLJ12629", "FLJ12631", "FLJ12633", "FLJ12635", "FLJ12637", "FLJ12639", "FLJ12641", "FLJ12643", "FLJ12645", "FLJ12647", "FLJ12649", "FLJ12651", "FLJ12653", "FLJ12655", "FLJ12657", "FLJ12659", "FLJ12661", "FLJ12663", "FLJ12665", "FLJ12667", "FLJ12669", "FLJ12671", "FLJ12673", "FLJ12675", "FLJ12677", "FLJ12679", "FLJ12681", "FLJ12683", "FLJ12685", "FLJ12687", "FLJ12689", "FLJ12691", "FLJ12693", "FLJ12695", "FLJ12697", "FLJ12699", "FLJ12701", "FLJ12703", "FLJ12705", "FLJ12707", "FLJ12709", "FLJ12711", "FLJ12713", "FLJ12715", "FLJ12717", "FLJ12719", "FLJ12721", "FLJ12723", "FLJ12725", "FLJ12727", "FLJ12729", "FLJ12731", "FLJ12733", "FLJ12735", "FLJ12737", "FLJ12739", "FLJ12741", "FLJ12743", "FLJ12745", "FLJ12747", "FLJ12749", "FLJ12751", "FLJ12753", "FLJ12755", "FLJ12757", "FLJ12759", "FLJ12761", "FLJ12763", "FLJ12765", "FLJ12767", "FLJ12769", "FLJ12771", "FLJ12773", "FLJ12775", "FLJ12777", "FLJ12779", "FLJ12781", "FLJ12783", "FLJ12785", "FLJ12787", "FLJ12789", "FLJ12791", "FLJ12793", "FLJ12795", "FLJ12797", "FLJ12799", "FLJ12801", "FLJ12803", "FLJ12805", "FLJ12807", "FLJ12809", "FLJ12811", "FLJ12813", "FLJ12815", "FLJ12817", "FLJ12819", "FLJ12821", "FLJ12823", "FLJ12825", "FLJ12827", "FLJ12829", "FLJ12831", "FLJ12833", "FLJ12835", "FLJ12837", "FLJ12839", "FLJ12841", "FLJ12843", "FLJ12845", "FLJ12847", "FLJ12849", "FLJ12851", "FLJ12853", "FLJ12855", "FLJ12857", "FLJ12859", "FLJ12861", "FLJ12863", "FLJ12865", "FLJ12867", "FLJ12869", "FLJ12871", "FLJ12873", "FLJ12875", "FLJ12877", "FLJ12879", "FLJ12881", "FLJ12883", "FLJ12885", "FLJ12887", "FLJ12889", "FLJ12891", "FLJ12893", "FLJ12895", "FLJ12897", "FLJ12899", "FLJ12901", "FLJ12903", "FLJ12905", "FLJ12907", "FLJ12909", "FLJ12911", "FLJ12913", "FLJ12915", "FLJ12917", "FLJ12919", "FLJ12921", "FLJ12923", "FLJ12925", "FLJ12927", "FLJ12929", "FLJ12931", "FLJ12933", "FLJ12935", "FLJ12937", "FLJ12939", "FLJ12941", "FLJ12943", "FLJ12945", "FLJ12947", "FLJ12949", "FLJ12951", "FLJ12953", "FLJ12955", "FLJ12957", "FLJ12959", "FLJ12961", "FLJ12963", "FLJ12965", "FLJ12967", "FLJ12969", "FLJ12971", "FLJ12973", "FLJ12975", "FLJ12977", "FLJ12979", "FLJ12981", "FLJ12983", "FLJ12985", "FLJ12987", "FLJ12989", "FLJ12991", "FLJ12993", "FLJ12995", "FLJ12997", "FLJ12999", "FLJ13001", "FLJ13003", "FLJ13005", "FLJ13007", "FLJ13009", "FLJ13011", "FLJ13013", "FLJ13015", "FLJ13017", "FLJ13019", "FLJ13021", "FLJ13023", "FLJ13025", "FLJ13027", "FLJ13029", "FLJ13031", "FLJ13033", "FLJ13035", "FLJ13037", "FLJ13039", "FLJ13041", "FLJ13043", "FLJ13045", "FLJ13047", "FLJ13049", "FLJ13051", "FLJ13053", "FLJ13055", "FLJ13057", "FLJ13059", "FLJ13061", "FLJ13063", "FLJ13065", "FLJ13067", "FLJ13069", "FLJ13071", "FLJ13073", "FLJ13075", "FLJ13077", "FLJ13079", "FLJ13081", "FLJ13083", "FLJ13085", "FLJ13087", "FLJ13089", "FLJ13091", "FLJ13093", "FLJ13095", "FLJ13097", "FLJ13099", "FLJ13101", "FLJ13103", "FLJ13105", "FLJ13107", "FLJ13109", "FLJ13111", "FLJ13113", "FLJ13115", "FLJ13117", "FLJ13119", "FLJ13121", "FLJ13123", "FLJ13125", "FLJ13127", "FLJ13129", "FLJ13131", "FLJ13133", "FLJ13135", "FLJ13137", "FLJ13139", "FLJ13141", "FLJ13143", "FLJ13145", "FLJ13147", "FLJ13149", "FLJ13151", "FLJ13153", "FLJ13155", "FLJ13157", "FLJ13159", "FLJ13161", "FLJ13163", "FLJ13165", "FLJ13167", "FLJ13169", "FLJ13171", "FLJ13173", "FLJ13175", "FLJ13177", "FLJ13179", "FLJ13181", "FLJ13183", "FLJ13185", "FLJ13187", "FLJ13189", "FLJ13191", "FLJ13193", "FLJ13195", "FLJ13197", "FLJ13199", "FLJ13201", "FLJ13203", "FLJ13205", "FLJ13207", "FLJ13209", "FLJ13211", "FLJ13213", "FLJ13215", "FLJ13217", "FLJ13219", "FLJ13221", "FLJ13223", "FLJ13225", "FLJ13227", "FLJ13229", "FLJ13231", "FLJ13233", "FLJ13235", "FLJ13237", "FLJ13239", "FLJ13241", "FLJ13243", "FLJ13245", "FLJ13247", "FLJ13249", "FLJ13251", "FLJ13253", "FLJ13255", "FLJ13257", "FLJ13259", "FLJ13261", "FLJ13263", "FLJ13265", "FLJ13267", "FLJ13269", "FLJ13271", "FLJ13273", "FLJ13275", "FLJ13277", "FLJ13279", "FLJ13281", "FLJ13283", "FLJ13285", "FLJ13287", "FLJ13289", "FLJ13291", "FLJ13293", "FLJ13295", "FLJ13297", "FLJ13299", "FLJ13301", "FLJ13303", "FLJ13305", "FLJ13307", "FLJ13309", "FLJ13311", "FLJ13313", "FLJ13315", "FLJ13317", "FLJ13319", "FLJ13321", "FLJ13323", "FLJ13325", "FLJ13327", "FLJ13329", "FLJ13331", "FLJ13333", "FLJ13335", "FLJ13337", "FLJ13339", "FLJ13341", "FLJ13343", "FLJ13345", "FLJ13347", "FLJ13349", "FLJ13351", "FLJ13353", "FLJ13355", "FLJ13357", "FLJ13359", "FLJ13361", "FLJ13363", "FLJ13365", "FLJ13367", "FLJ13369", "FLJ13371", "FLJ13373", "FLJ13375", "FLJ13377", "FLJ13379", "FLJ13381", "FLJ13383", "FLJ13385", "FLJ13387", "FLJ13389", "FLJ13391", "FLJ13393", "FLJ13395", "FLJ13397", "FLJ13399", "FLJ13401", "FLJ13403", "FLJ13405", "FLJ13407", "FLJ13409", "FLJ13411", "FLJ13413", "FLJ13415", "FLJ13417", "FLJ13419", "FLJ13421", "FLJ13423", "FLJ13425", "FLJ1
```

--------------------------------

### Get Clinical Data by Sample

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Retrieves sample-level clinical data for specific sample IDs within a given study. It supports fetching all attributes or specific ones, and can query across multiple studies using sample-study pairs.

```r
# Get clinical data for specific samples
samples <- c("TCGA-OR-A5J2-01", "TCGA-OR-A5J6-01")

clinical <- get_clinical_by_sample(
  sample_id = samples,
  study_id = "acc_tcga"
)

# Get specific attributes
clinical <- get_clinical_by_sample(
  sample_id = samples,
  study_id = "acc_tcga",
  clinical_attribute = c("CANCER_TYPE", "MUTATION_COUNT", "FRACTION_GENOME_ALTERED")
)

# Query across multiple studies using sample_study_pairs
df_pairs <- data.frame(
  sample_id = c("P-0001453-T01-IM3", "P-0002166-T01-IM3", "s_C_36924L_P001_d"),
  study_id = c("blca_nmibc_2017", "blca_nmibc_2017", "prad_msk_2019")
)

multi_study_clinical <- get_clinical_by_sample(sample_study_pairs = df_pairs)
```

--------------------------------

### Get Segmentation Data by Sample

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Retrieves segmentation data for specified sample IDs within a given study. This is useful for analyzing copy number alterations.

```r
segments <- get_segments_by_sample(
  sample_id = c("s_C_CAUWT7_P001_d"),
  study_id = "prad_msk_2019"
)
```

--------------------------------

### Direct cBioPortal API Access with cbp_api

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Provides low-level access to the cBioPortal API for custom queries. Supports both GET and POST requests, allowing for flexible data retrieval beyond the standard wrapper functions. Requires specifying the URL path, method, and optionally a base URL and request body.

```r
# Direct API call - GET request
result <- cbp_api(
  url_path = "genes/TP53",
  base_url = "public"
)
result$content
#> $entrezGeneId
#> [1] 7157
#> $hugoGeneSymbol
#> [1] "TP53"
#> $type
#> [1] "protein-coding"

# POST request with body
result <- cbp_api(
  url_path = "genes/fetch?geneIdType=HUGO_GENE_SYMBOL",
  method = "post",
  body = c("TP53", "BRCA1", "BRCA2"),
  base_url = "public"
)

# Access raw API response
result$response$status_code
result$path
```

--------------------------------

### Get Samples by Patient

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Returns all sample IDs associated with a given patient ID within a specific study. This is useful for identifying all samples belonging to a single patient.

```r
# Get all samples for specific patients
samples <- get_samples_by_patient(
  patient_id = c("P-0000034", "P-0000036"),
  study_id = "msk_impact_2017"
)
samples
```

--------------------------------

### Get Entrez ID from Hugo Symbol

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Converts Hugo Symbols to Entrez Gene IDs.

```APIDOC
## GET /api/genes/entrez_id

### Description
Converts Hugo Symbols to Entrez Gene IDs.

### Method
GET

### Endpoint
/api/genes/entrez_id

### Parameters
#### Query Parameters
- **hugo_symbol** (string array) - Required - A list of Hugo Symbols.

### Request Example
```json
{
  "hugo_symbol": ["FGFR1", "TP53"]
}
```

### Response
#### Success Response (200)
- **data** (array) - A list of gene objects, each containing `entrezGeneId`, `hugoGeneSymbol`, and `type`.

#### Response Example
```json
{
  "data": [
    { "entrezGeneId": 2260, "hugoGeneSymbol": "FGFR1", "type": "protein-coding" },
    { "entrezGeneId": 7157, "hugoGeneSymbol": "TP53", "type": "protein-coding" }
  ]
}
```
```

--------------------------------

### Get Hugo Symbol from Entrez ID

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Converts Entrez Gene IDs to Hugo Symbols.

```APIDOC
## GET /api/genes/hugo_symbol

### Description
Converts Entrez Gene IDs to Hugo Symbols.

### Method
GET

### Endpoint
/api/genes/hugo_symbol

### Parameters
#### Query Parameters
- **entrez_id** (string array) - Required - A list of Entrez Gene IDs.

### Request Example
```json
{
  "entrez_id": ["2261", "7157"]
}
```

### Response
#### Success Response (200)
- **data** (array) - A list of gene objects, each containing `entrezGeneId`, `hugoGeneSymbol`, and `type`.

#### Response Example
```json
{
  "data": [
    { "entrezGeneId": 2261, "hugoGeneSymbol": "FGFR3", "type": "protein-coding" },
    { "entrezGeneId": 7157, "hugoGeneSymbol": "TP53", "type": "protein-coding" }
  ]
}
```
```

--------------------------------

### Get Gene Panel by Sample

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Retrieves the gene panel information used for sequencing specific samples within a given study. This helps in understanding the scope of genomic data available for a sample.

```r
# Get gene panel information for samples
panel_info <- get_panel_by_sample(
  sample_id = "DS-sig-010-P2",
  study_id = "blca_plasmacytoid_mskcc_2016"
)
panel_info
```

--------------------------------

### Get Clinical Data by Patient

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Retrieves patient-level clinical data for specific patients, optionally filtering by clinical attributes or querying across multiple studies.

```APIDOC
## GET /api/clinical/by_patient

### Description
Retrieves patient-level clinical data for specific patients.

### Method
GET

### Endpoint
/api/clinical/by_patient

### Parameters
#### Query Parameters
- **patient_id** (string array) - Required (if `patient_study_pairs` is not provided) - A list of patient IDs.
- **study_id** (string) - Required (if `patient_study_pairs` is not provided) - The ID of the study.
- **patient_study_pairs** (object array) - Required (if `patient_id` and `study_id` are not provided) - An array of objects, where each object contains `patient_id` and `study_id`.
- **clinical_attribute** (string array) - Optional - A list of specific clinical attributes to retrieve.

### Request Example
```json
{
  "patient_id": ["TCGA-OR-A5J2", "TCGA-OR-A5J6"],
  "study_id": "acc_tcga",
  "clinical_attribute": "AGE"
}
```

### Response
#### Success Response (200)
- **data** (object) - Patient-level clinical data.

#### Response Example
```json
{
  "data": { ... clinical data ... }
}
```
```

--------------------------------

### Get Gene Aliases

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Retrieves known gene aliases for a given Hugo Symbol. This can be helpful for identifying alternative names used for a gene in different contexts.

```r
# Get gene alias information for a gene
# Note: The actual function call for get_alias is missing in the provided text.
```

--------------------------------

### Get All Genes

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Retrieves a comprehensive list of all genes available in the cBioPortal database, including their Entrez Gene IDs and Hugo Symbols. This function is useful for exploring the gene universe covered by cBioPortal.

```r
# Get all genes in the database
all_genes <- get_genes()
all_genes
```

--------------------------------

### Get Gene Panel Information using cbioportalR

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Fetches detailed information about genes included in a specified gene panel. Supports retrieving genes for a single panel or multiple panels by providing a vector of panel IDs.

```r
# Get genes in a panel
impact_genes <- get_gene_panel(panel_id = "IMPACT468")
impact_genes
#> # A tibble: 468 × 4
#>    genePanelId entrezGeneId hugoGeneSymbol description
#>    <chr>              <int> <chr>          <chr>
#>  1 IMPACT468             25 ABL1           MSK-IMPACT (468 genes)
#>  2 IMPACT468            238 ALK            MSK-IMPACT (468 genes)
#> # ℹ more rows

# Get multiple panels
panels <- get_gene_panel(panel_id = c("IMPACT468", "IMPACT341"))
```

--------------------------------

### Get Clinical Data by Patient

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Retrieves patient-level clinical data for specific patient IDs within a given study. This function can fetch all attributes or specific ones and supports querying across multiple studies using patient-study pairs.

```r
# Get clinical data for specific patients
patients <- c("TCGA-OR-A5J2", "TCGA-OR-A5J6")

clinical <- get_clinical_by_patient(
  patient_id = patients,
  study_id = "acc_tcga",
  clinical_attribute = "AGE"
)

# Query across multiple studies
patient_pairs <- data.frame(
  patient_id = c("P-0001453", "P-0002166", "P-0000004"),
  study_id = c("blca_nmibc_2017", "blca_nmibc_2017", "msk_impact_2017")
)

multi_clinical <- get_clinical_by_patient(
  patient_study_pairs = patient_pairs,
  clinical_attribute = c("AGE", "SEX")
)
```

--------------------------------

### Get Genomic Data by Study ID in R

Source: https://github.com/karissawhiting/cbioportalr/blob/main/README.md

This function retrieves all available genomic data (mutations, CNA, and optionally fusion data) for a given study ID from cBioPortal. It returns a list of data frames, one for each data type. Note that fusion data may not be available for all studies.

```r
df <- get_genetics_by_study(study_id = "acc_tcga")
```

--------------------------------

### Get Specific Study Metadata in R

Source: https://github.com/karissawhiting/cbioportalr/blob/main/README.md

This R code snippet shows how to fetch detailed metadata for a specific study, identified by its ID (e.g., 'acc_tcga'). It uses the `get_study_info()` function and then transposes the resulting list into a matrix for easier viewing of the study's properties and their values.

```r
get_study_info("acc_tcga") %>%
  t()
```

--------------------------------

### Get Gene Aliases using cbioportalR

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Retrieves alternative gene symbols (aliases) for given HUGO gene symbols. This function is useful for mapping gene identifiers and ensuring comprehensive data analysis.

```r
aliases <- get_alias(hugo_symbol = c("FGFR3", "TP53"))
aliasest
#> # A tibble: 6 × 2
#>   hugo_symbol alias
#>   <chr>       <chr>
#> 1 FGFR3       ACH
#> 2 FGFR3       CD333
#> 3 TP53        p53
#> 4 TP53        LFS1
```

--------------------------------

### Configure R Environment Variables

Source: https://github.com/karissawhiting/cbioportalr/blob/main/README.md

Opens the .Renviron file for editing and demonstrates the format for storing the CBIOPORTAL_TOKEN environment variable.

```r
usethis::edit_r_environ()
CBIOPORTAL_TOKEN = 'YOUR_TOKEN'
```

--------------------------------

### Set and Test Database Connection

Source: https://github.com/karissawhiting/cbioportalr/blob/main/README.md

Configures the target cBioPortal database URL and verifies the connection status to ensure API calls will succeed.

```r
set_cbioportal_db(db = "public")
test_cbioportal_db()
```

--------------------------------

### Authentication and Database Connection

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Functions for setting up the cBioPortal database connection and handling authentication tokens.

```APIDOC
## Authentication and Database Connection

### set_cbioportal_db

Sets the cBioPortal database URL for the current R session. This function must be called at the start of each session to establish the connection to the cBioPortal API. It validates the connection and stores the URL as an environment variable for all subsequent API calls.

### Method

`set_cbioportal_db`

### Parameters

#### Query Parameters

- **db** (string) - Required - The URL or identifier for the cBioPortal database (e.g., "public", "cbioportal.mskcc.org", "https://www.cbioportal.org").

### Request Example

```R
library(cbioportalR)

# Connect to the public cBioPortal database
set_cbioportal_db(db = "public")
#> ✔ You are successfully connected!
#> ✔ base_url for this R session is now set to "www.cbioportal.org/api"

# Or connect to a private institutional instance
set_cbioportal_db(db = "cbioportal.mskcc.org")

# Using full URL
set_cbioportal_db(db = "https://www.cbioportal.org")
```

### get_cbioportal_token

Retrieves the cBioPortal authentication token from the CBIOPORTAL_TOKEN environment variable stored in .Renviron. This is required only for private cBioPortal instances that require authentication.

### Method

`get_cbioportal_token`

### Parameters

None

### Request Example

```R
# Check if token is properly configured
token <- get_cbioportal_token()

# If no token is found, you'll receive a warning
# To set up a token, add to your .Renviron file:
# CBIOPORTAL_TOKEN = 'your_token_here'

# You can easily open .Renviron with:
# usethis::edit_r_environ()
```

### test_cbioportal_db

Tests the current database connection at any point during your R session. Useful for troubleshooting API issues or verifying connectivity after network changes.

### Method

`test_cbioportal_db`

### Parameters

None

### Request Example

```R
# Verify connection is still active
test_cbioportal_db()
#> ✔ You are successfully connected!
```
```

--------------------------------

### Retrieve Mutations by Sample

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Fetches mutation data for specific samples with options to filter by Hugo symbol, Entrez ID, or gene panel.

```R
mutations <- get_mutations_by_sample(sample_id = c("TCGA-OR-A5J2-01", "TCGA-OR-A5J6-01"), study_id = "acc_tcga")
tp53_mutations <- get_mutations_by_sample(sample_id = c("TCGA-OR-A5J2-01", "TCGA-OR-A5J6-01"), study_id = "acc_tcga", genes = "TP53")
```

--------------------------------

### Verify Authentication Token

Source: https://github.com/karissawhiting/cbioportalr/blob/main/README.md

Checks if the cBioPortal token has been correctly loaded into the current R session environment.

```r
get_cbioportal_token()
```

--------------------------------

### Verify Database Connection

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Tests the current active connection to the cBioPortal database. Useful for troubleshooting and ensuring the API is reachable.

```R
test_cbioportal_db()
```

--------------------------------

### Available Samples API

Source: https://github.com/karissawhiting/cbioportalr/blob/main/README.md

Lists the samples available within a specified study.

```APIDOC
## GET /api/studies/{study_id}/samples

### Description
Lists the samples available within a specified study.

### Method
GET

### Endpoint
/api/studies/{study_id}/samples

### Parameters
#### Path Parameters
- **study_id** (string) - Required - The ID of the study to retrieve samples from.

### Request Example
```r
available_samples <- available_samples(study_id = "acc_tcga")
```

### Response
#### Success Response (200)
- **samples** (list) - A list of available samples within the study.

#### Response Example
```json
[
  "SAMPLE1",
  "SAMPLE2",
  "SAMPLE3"
]
```
```

--------------------------------

### Load cbioportalR Package

Source: https://github.com/karissawhiting/cbioportalr/blob/main/README.md

R code to load the cbioportalR package into the current R session for use.

```r
library(cbioportalR)
```

--------------------------------

### Retrieve CNA Data by Sample

Source: https://context7.com/karissawhiting/cbioportalr/llms.txt

Fetches CNA data for specific samples, with optional filtering for specific oncogenes.

```R
cna_data <- get_cna_by_sample(sample_id = c("s_C_36924L_P001_d"), study_id = "prad_msk_2019")
onco_cna <- get_cna_by_sample(sample_id = c("s_C_36924L_P001_d"), study_id = "prad_msk_2019", genes = c("AR", "MYC", "PTEN", "RB1"))
```

--------------------------------

### Retrieve Mutations by Sample

Source: https://github.com/karissawhiting/cbioportalr/blob/main/README.md

Fetches mutation data for specified samples within a given study ID. It returns a tibble containing genomic details like gene symbols and mutation types.

```R
mutations <- get_mutations_by_sample(sample_id = samples, study_id = "acc_tcga")
mutations %>% head()
```