### Install UCSCXenaTools with Vignettes

Source: https://github.com/ropensci/ucscxenatools/blob/master/README.md

Installs the development version of the UCSCXenaTools package from GitHub, including building vignettes. This option also installs all necessary dependencies.

```r
remotes::install_github("ropensci/UCSCXenaTools", build_vignettes = TRUE, dependencies = TRUE)
```

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

### Install UCSCXenaTools Development Version

Source: https://github.com/ropensci/ucscxenatools/blob/master/README.md

Installs the development version of the UCSCXenaTools package directly from GitHub. This is useful for accessing the latest features or bug fixes.

```r
# install.packages("remotes")
remotes::install_github("ropensci/UCSCXenaTools")
```

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

### Install UCSCXenaTools from CRAN

Source: https://github.com/ropensci/ucscxenatools/blob/master/README.md

Installs the stable release of the UCSCXenaTools package from the r-universe/CRAN repository. Ensure you have the necessary repositories configured.

```r
install.packages('UCSCXenaTools', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))
```

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

### Get available TCGA File Types

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Call availTCGA("FileType") to see the various file formats in which TCGA data is stored. This is important for selecting the correct format for downstream analysis.

```r
# Get all available file types
availTCGA("FileType")
```

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

### Get available TCGA Project IDs

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Use availTCGA("ProjectID") to retrieve a list of all available TCGA project identifiers. This helps in identifying which cancer projects are available in the TCGA dataset.

```r
library(UCSCXenaTools)

# Get all available project IDs
availTCGA("ProjectID")
#> [1] "LAML" "ACC" "CHOL" "BLCA" "BRCA" "CESC" "COADREAD" "COAD" "UCEC"
#> [10] "ESCA" "FPPP" "GBM" "HNSC" "KICH" "KIRC" "KIRP" "DLBC" "LIHC"
#> ...
```

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

### Get available TCGA Data Types

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Use availTCGA("DataType") to list all the different types of data available for TCGA projects, such as gene expression or copy number variations. This is useful for understanding the omics data available.

```r
# Get all available data types
availTCGA("DataType")
#> [1] "Gene Level Copy Number" "Copy Number Segments" "DNA Methylation"
#> [4] "Exon Expression RNASeq" "Gene Expression Array" "Gene Expression RNASeq"
#> ...
```

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

### Load Data into R with XenaPrepare

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Loads downloaded datasets into R as tibbles. Can accept output from XenaDownload, file paths, directories, or URLs. Supports chunked reading for large files and subsetting rows.

```r
library(UCSCXenaTools)

# Complete workflow ending with data preparation
XenaGenerate(subset = XenaHostNames == "tcgaHub") %>%
  XenaFilter(filterDatasets = "clinical") %>%
  XenaFilter(filterDatasets = "LUAD|LUSC|LUNG") %>%
  XenaQuery() %>%
  XenaDownload() -> xe_download

# Load downloaded data into R
cli <- XenaPrepare(xe_download)
class(cli)
#> [1] "list"
names(cli)
#> [1] "LUNG_clinicalMatrix" "LUAD_clinicalMatrix" "LUSC_clinicalMatrix"
```

```r
# Load from local file paths
cli_data <- XenaPrepare("/path/to/downloaded/file.tsv")
```

```r
# Load from directory
cli_data <- XenaPrepare("/path/to/download/directory/")
```

```r
# Load with chunked reading for large files
cli_large <- XenaPrepare(
  xe_download,
  use_chunk = TRUE,
  chunk_size = 1000,
  select_cols = colnames(x)[1:5]
)
```

```r
# Subset rows while loading
cli_subset <- XenaPrepare(
  xe_download,
  use_chunk = TRUE,
  subset_rows = sample == "TCGA-02-0047-01"
)
```

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

### Query and Download Selected Datasets

Source: https://github.com/ropensci/ucscxenatools/blob/master/README.md

Query the selected datasets from the XenaHub object and then initiate the download of these datasets. The process includes checks for URL status and specifies the directory for downloaded files.

```r
XenaQuery(df_todo) %>%
  XenaDownload() -> xe_download
#> This will check url status, please be patient.
#> All downloaded files will under directory /var/folders/h0/s_35svc15n1glmp65lbbkx9w0000gn/T//RtmpmgBjSb.
#> The 'trans_slash' option is FALSE, keep same directory structure as Xena.
#> Creating directories for datasets...
#> Downloading TCGA.LUNG.sampleMap/LUNG_clinicalMatrix
#> Downloading TCGA.LUAD.sampleMap/LUAD_clinicalMatrix
#> Downloading TCGA.LUSC.sampleMap/LUSC_clinicalMatrix
```

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

### Prepare Downloaded Data for Analysis

Source: https://github.com/ropensci/ucscxenatools/blob/master/README.md

Prepare the downloaded Xena data into an R list format suitable for analysis. This function processes the downloaded files and returns a list where each element corresponds to a dataset.

```r
cli = XenaPrepare(xe_download)
class(cli)
#> [1] "list"
names(cli)
#> [1] "LUNG_clinicalMatrix" "LUAD_clinicalMatrix" "LUSC_clinicalMatrix"
```

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

### availTCGA - List Available TCGA Data Options

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Lists available TCGA project IDs, data types, and file types.

```APIDOC
## availTCGA - List Available TCGA Data Options

### Description
Lists available TCGA project IDs, data types, and file types.

### Method
GET

### Endpoint
/api/v1/availTCGA

### Parameters
#### Query Parameters
- **category** (string) - Optional - The category to list ('all', 'ProjectID', 'DataType', 'FileType'). Defaults to 'all'.

### Response
#### Success Response (200)
- **options** (object) - An object containing lists of available TCGA options.

#### Response Example
```json
{
  "ProjectID": ["LAML", "ACC", "CHOL", ...],
  "DataType": ["Gene Level Copy Number", "Copy Number Segments", ...],
  "FileType": ["Gistic2", "Gistic2 thresholded", ...]
}
```
```

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

### Show TCGA data structure for all projects

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Execute showTCGA("all") to view the data structure, including data types and file types, for all available TCGA projects. This provides a comprehensive overview of the TCGA data landscape.

```r
# Show all projects
showTCGA("all")
```

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

### XenaHub - Direct Hub Access

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Creates a XenaHub object by directly querying UCSC Xena hosts. Useful for real-time data access.

```APIDOC
## XenaHub - Direct Hub Access

### Description
Creates a XenaHub object by directly querying UCSC Xena hosts. This is useful when you need real-time data from the hubs rather than using the built-in XenaData.

### Method
GET

### Endpoint
/api/v1/XenaHub

### Parameters
#### Query Parameters
- **hostName** (string) - Optional - The name or URL of the Xena hub to connect to.
- **cohorts** (string or array of strings) - Optional - Specifies the cohorts to retrieve.
- **datasets** (string or array of strings) - Optional - Specifies the datasets to retrieve.

### Request Example
```json
{
  "hostName": "tcgaHub",
  "cohorts": "Cancer Cell Line Encyclopedia (CCLE)"
}
```

### Response
#### Success Response (200)
- **XenaHub object** - An object representing the Xena hub connection, with methods to access hosts, cohorts, datasets, and samples.

#### Response Example (Accessing hosts)
```json
["https://ucscpublic.xenahubs.net", "https://tcga.xenahubs.net"]
```
```

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

### Query Dataset Download URLs

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Queries and checks the availability of download URLs for datasets within a XenaHub object. Returns a data frame containing hosts, datasets, and their corresponding download URLs.

```r
library(UCSCXenaTools)

# Create a XenaHub object and query URLs
XenaGenerate(subset = XenaHostNames == "tcgaHub") %>%
  XenaFilter(filterDatasets = "clinical") %>%
  XenaFilter(filterDatasets = "LUAD") -> xe

xe_query <- XenaQuery(xe)
#> This will check url status, please be patient.
```

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

### Download Datasets with XenaDownload

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Downloads datasets from UCSC Xena hubs. Supports specifying destination directory, forcing re-downloads, and downloading associated ProbeMap files.

```r
library(UCSCXenaTools)

# Complete workflow: generate, filter, query, download
XenaGenerate(subset = XenaHostNames == "tcgaHub") %>%
  XenaFilter(filterDatasets = "clinical") %>%
  XenaFilter(filterDatasets = "LUAD|LUSC") %>%
  XenaQuery() %>%
  XenaDownload(destdir = tempdir()) -> xe_download

#> This will check url status, please be patient.
#> All downloaded files will under directory /tmp/...
#> Creating directories for datasets...
#> Downloading TCGA.LUAD.sampleMap/LUAD_clinicalMatrix
#> Downloading TCGA.LUSC.sampleMap/LUSC_clinicalMatrix
```

```r
# Download with ProbeMap for gene mapping
XenaGenerate(subset = XenaHostNames == "tcgaHub") %>%
  XenaFilter(filterDatasets = "HiSeqV2$") %>%
  XenaFilter(filterCohorts = "LUAD") %>%
  XenaQuery() %>%
  XenaDownload(destdir = "~/xena_data/", download_probeMap = TRUE)
```

```r
# Force re-download even if files exist
XenaDownload(xe_query, destdir = "~/xena_data/", force = TRUE)
```

```r
# Resume download from breakpoint using curl
XenaDownload(xe_query, destdir = "~/xena_data/", method = "curl", extra = "-C - -L")
```

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

### Generate XenaHub Objects

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Creates a XenaHub object, which represents a connection to a UCSC Xena hub. Supports subsetting by host, cohort, or dataset using logical expressions.

```r
library(UCSCXenaTools)

# Generate a XenaHub object with all datasets
xe_all <- XenaGenerate()
xe_all
#> class: XenaHub
#> hosts():
#>   https://ucscpublic.xenahubs.net
#>   https://tcga.xenahubs.net
#>   ...

# Generate XenaHub for specific data hub
xe_tcga <- XenaGenerate(subset = XenaHostNames == "tcgaHub")
xe_tcga
#> class: XenaHub
#> hosts():
#>   https://tcga.xenahubs.net

# Generate XenaHub for specific cohort
xe_brca <- XenaGenerate(subset = XenaCohorts == "TCGA Breast Cancer (BRCA)")

# Generate XenaHub using pattern matching
xe_lung <- XenaGenerate(subset = grepl("LUNG", XenaCohorts))
```

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

### Scan XenaData for Datasets by Keyword

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Searches the XenaData data frame for datasets matching a specified keyword pattern. Useful for finding data when only partial information is known. Results can be converted to XenaHub objects.

```r
library(UCSCXenaTools)

# Scan for datasets containing "Blood"
x1 <- XenaScan(pattern = "Blood")

# Case-sensitive search for "LUNG"
x2 <- XenaScan(pattern = "LUNG", ignore.case = FALSE)

# Convert scan results to XenaHub objects
x1 %>%
  XenaGenerate()
x2 %>%
  XenaGenerate()

# Search for specific gene or feature
x_tp53 <- XenaScan(pattern = "TP53")
```

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

### Fetch Sparse Mutation Data

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Fetches mutation data from sparse datasets for specified genes and samples. Requires host, dataset, and gene identifiers.

```r
library(UCSCXenaTools)

# Query mutation data from CCLE
host <- "https://ucscpublic.xenahubs.net"
dataset <- "ccle/CCLE_DepMap_18Q2_maf_20180502"
genes <- c("TP53", "KRAS", "BRAF")

mutation_data <- fetch_sparse_values(
  host = host,
  dataset = dataset,
  genes = genes
)

# Result contains mutation information per sample
str(mutation_data)
```

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

### List of Datasets in UCSCXenaTools

Source: https://github.com/ropensci/ucscxenatools/blob/master/NEWS.md

This R code snippet displays a list of dataset filenames included in the UCSCXenaTools package. It is useful for understanding the available data resources.

```r
[1] "TCGA_survival_data_2.txt"                                  
[2] "clinical_CellLinePolyA_21.06_2021-06-15.tsv"               
[3] "CellLinePolyA_21.06_hugo_log2tpm_58581genes_2021-06-15.tsv"
```

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

### Direct Xena Hub Access

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Creates a XenaHub object for direct querying of UCSC Xena hosts. Useful for real-time data access. Allows access to hosts, cohorts, datasets, and samples.

```r
library(UCSCXenaTools)

# Get all available hosts
xena_default_hosts()
#> [1] "https://ucscpublic.xenahubs.net" "https://tcga.xenahubs.net"
#> [3] "https://gdc.xenahubs.net" "https://icgc.xenahubs.net"
#> ...

# Create XenaHub for specific host
xe <- XenaHub(hostName = "tcgaHub")

# Access XenaHub components
hosts(xe)      # Get hosts
cohorts(xe)    # Get cohorts
datasets(xe)   # Get datasets

# Get samples for a cohort
xe_ccle <- XenaHub(cohorts = "Cancer Cell Line Encyclopedia (CCLE)")
sample_list <- samples(xe_ccle, by = "datasets", how = "each")
```

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

### Fetch Dataset Samples and Identifiers

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Retrieve sample IDs and identifiers (probes/genes) from a dataset without downloading the full data. Supports limiting the number of results.

```r
library(UCSCXenaTools)

host <- "https://toil.xenahubs.net"
dataset <- "tcga_RSEM_gene_tpm"

# Get all sample IDs from a dataset
all_samples <- fetch_dataset_samples(host, dataset)
length(all_samples)
#> [1] 10535

# Get first 10 samples
sample_subset <- fetch_dataset_samples(host, dataset, limit = 10)
```

```r
# Get all identifiers (probes/genes) from a dataset
all_identifiers <- fetch_dataset_identifiers(host, dataset)
length(all_identifiers)
#> [1] 60498

head(all_identifiers)
#> [1] "ENSG00000000003.14" "ENSG00000000005.5" "ENSG00000000419.12"
```

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

### Open Dataset or Cohort in Xena Browser

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Opens the UCSC Xena web page for a specific dataset or cohort in the default browser. Can open single or multiple datasets/cohorts.

```r
library(UCSCXenaTools)

# Create a XenaHub object with single dataset
XenaGenerate(subset = XenaHostNames == "tcgaHub") %>%
  XenaFilter(filterDatasets = "clinical") %>%
  XenaFilter(filterDatasets = "LUAD") -> to_browse

# Open dataset page in browser
XenaBrowse(to_browse)

# Open cohort page in browser
XenaBrowse(to_browse, type = "cohort")

# Browse multiple datasets
XenaGenerate(subset = XenaHostNames == "tcgaHub") %>%
  XenaFilter(filterDatasets = "clinical") %>%
  XenaFilter(filterDatasets = "LUAD|LUSC") -> to_browse_multi

XenaBrowse(to_browse_multi, multiple = TRUE)
```

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

### showTCGA - Show TCGA Data Information

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Shows available data types and file types for a given TCGA project.

```APIDOC
## showTCGA - Show TCGA Data Information

### Description
Shows available data types and file types for a given TCGA project.

### Method
GET

### Endpoint
/api/v1/showTCGA

### Parameters
#### Query Parameters
- **project** (string) - Required - The TCGA project ID (e.g., "LUAD").

### Response
#### Success Response (200)
- **data_info** (table) - A table listing the available Data Types and File Types for the specified project.

#### Response Example
```json
[
  {
    "ProjectID": "LUAD",
    "DataType": "Gene Level Copy Number",
    "FileType": "Gistic2"
  },
  {
    "ProjectID": "LUAD",
    "DataType": "Gene Level Copy Number",
    "FileType": "Gistic2 thresholded"
  }
]
```
```

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

### Load and Inspect XenaData

Source: https://github.com/ropensci/ucscxenatools/blob/master/README.md

Load the XenaData data frame from the UCSCXenaTools package and display the first few rows to understand its structure and content. This data frame contains information about datasets available in UCSC Xena Hubs.

```r
library(UCSCXenaTools)
# =========================================================================================
# UCSCXenaTools version 1.6.0
# Project URL: https://github.com/ropensci/UCSCXenaTools
# Usages: https://cran.r-project.org/web/packages/UCSCXenaTools/vignettes/USCSXenaTools.html
# 
# If you use it in published research, please cite:
# Wang et al., (2019). The UCSCXenaTools R package: a toolkit for accessing genomics data
#   from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq.
#   Journal of Open Source Software, 4(40), 1627, https://doi.org/10.21105/joss.01627
# =========================================================================================
#                               --Enjoy it--
data(XenaData)

head(XenaData)
# # A tibble: 6 × 17
#   XenaHosts XenaHostNames XenaCohorts XenaDatasets SampleCount DataSubtype Label
#   <chr>     <chr>         <chr>       <chr>              <int> <chr>       <chr>
# 1 https://… publicHub     Breast Can… ucsfNeve_pu…          51 gene expre… Neve…
# 2 https://… publicHub     Breast Can… ucsfNeve_pu…          57 phenotype   Phen…
# 3 https://… publicHub     Glioma (Ko… kotliarov20…         194 copy number Kotl…
# 4 https://… publicHub     Glioma (Ko… kotliarov20…         194 phenotype   Phen…
# 5 https://… publicHub     Lung Cance… weir2007_pu…         383 copy number CGH  
# 6 https://… publicHub     Lung Cance… weir2007_pu…         383 phenotype   Phen…
# # ℹ 10 more variables: Type <chr>, AnatomicalOrigin <chr>, SampleType <chr>,
# #   Tags <chr>, ProbeMap <chr>, LongTitle <chr>, Citation <chr>, Version <chr>,
# #   Unit <chr>, Platform <chr>
```

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

### Load and Explore XenaData Metadata

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Loads the built-in XenaData data frame containing metadata for all available datasets. Use `head()` to view the first few rows and `colnames()` to check available columns.

```r
library(UCSCXenaTools)

# Load the built-in dataset information
data(XenaData)

# Explore the structure
head(XenaData)
#> # A tibble: 6 x 17
#>   XenaHosts XenaHostNames XenaCohorts XenaDatasets SampleCount DataSubtype Label
#>   <chr>     <chr>         <chr>       <chr>              <int> <chr>       <chr>
#> 1 https://... publicHub   Breast Can... ucsfNeve_pu...     51 gene expre... Neve...
#> 2 https://... publicHub   Breast Can... ucsfNeve_pu...     57 phenotype   Phen...

# Check available columns
colnames(XenaData)
#> [1] "XenaHosts" "XenaHostNames" "XenaCohorts" "XenaDatasets" "SampleCount"
#> [6] "DataSubtype" "Label" "Type" "AnatomicalOrigin" "SampleType"
#> [11] "Tags" "ProbeMap" "LongTitle" "Citation" "Version" "Unit" "Platform"
```

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

### fetch_sparse_values - Query Mutation Data

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Fetches mutation data from sparse datasets for specified genes and samples.

```APIDOC
## fetch_sparse_values - Query Mutation Data

### Description
Fetches mutation data from sparse datasets for specified genes and samples.

### Method
POST

### Endpoint
/api/v1/fetchSparseValues

### Parameters
#### Query Parameters
- **host** (string) - Required - The base URL of the Xena hub.
- **dataset** (string) - Required - The identifier of the dataset.
- **genes** (array of strings) - Required - A list of gene symbols to query.

### Request Example
```json
{
  "host": "https://ucscpublic.xenahubs.net",
  "dataset": "ccle/CCLE_DepMap_18Q2_maf_20180502",
  "genes": ["TP53", "KRAS", "BRAF"]
}
```

### Response
#### Success Response (200)
- **mutation_data** (object) - An object containing mutation information per sample.

#### Response Example
```json
{
  "sample1": {
    "TP53": "Mutated",
    "KRAS": "Wildtype",
    "BRAF": "Mutated"
  },
  "sample2": {
    "TP53": "Wildtype",
    "KRAS": "Mutated",
    "BRAF": "Wildtype"
  }
}
```
```

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

### Show TCGA data structure for a specific project

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Use showTCGA("ProjectID") to display the available data types and file types for a particular TCGA project. Replace 'BRCA' with the desired project ID.

```r
# Show data structure for specific projects
showTCGA("BRCA")
#>   ProjectID                          DataType                        FileType
#> 1      BRCA           Gene Level Copy Number                          Gistic2
#> 2      BRCA           Gene Level Copy Number               Gistic2 thresholded
#> 3      BRCA              Copy Number Segments       Before remove germline cnv
#> ...
```

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

### downloadTCGA - Direct TCGA Download

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Provides direct download of TCGA data by specifying project, data type, and file type explicitly.

```APIDOC
## downloadTCGA - Direct TCGA Download

### Description
Provides direct download of TCGA data by specifying project, data type, and file type explicitly.

### Method
GET

### Endpoint
/api/v1/downloadTCGA

### Parameters
#### Query Parameters
- **project** (string) - Required - The TCGA project ID (e.g., "UVM").
- **data_type** (string) - Required - The type of data to download (e.g., "Gene Expression RNASeq").
- **file_type** (string) - Required - The file type of the data (e.g., "IlluminaHiSeq RNASeqV2").
- **destdir** (string) - Optional - The destination directory for downloaded files.

### Request Example
```json
{
  "project": "UVM",
  "data_type": "Gene Expression RNASeq",
  "file_type": "IlluminaHiSeq RNASeqV2",
  "destdir": "~/tcga_data/"
}
```
```

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

### getTCGAdata - Simplified TCGA Download

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Provides a simplified interface for downloading common TCGA datasets by project ID and data type.

```APIDOC
## getTCGAdata - Simplified TCGA Download

### Description
Provides a simplified interface for downloading common TCGA datasets by project ID and data type, similar to RTCGAToolbox's getFirehoseData.

### Method
GET

### Endpoint
/api/v1/getTCGAdata

### Parameters
#### Query Parameters
- **project** (string or array of strings) - Required - The TCGA project ID(s) (e.g., "LUAD").
- **clinical** (boolean) - Optional - Whether to download clinical data.
- **mRNASeq** (boolean) - Optional - Whether to download mRNASeq data.
- **mRNASeqType** (string or array of strings) - Optional - Type(s) of mRNASeq data to download (e.g., "normalized").
- **Methylation** (boolean) - Optional - Whether to download methylation data.
- **MethylationType** (string) - Optional - Type of methylation data to download (e.g., "450K").
- **GeneMutation** (boolean) - Optional - Whether to download gene mutation data.
- **RPPAArray** (boolean) - Optional - Whether to download RPPA array data.
- **download** (boolean) - Optional - If TRUE, downloads the data. Defaults to FALSE.
- **destdir** (string) - Optional - The destination directory for downloaded files.

### Request Example
```json
{
  "project": "LUAD",
  "clinical": true,
  "mRNASeq": true,
  "mRNASeqType": "normalized",
  "GeneMutation": true,
  "download": false
}
```

### Response
#### Success Response (200)
- **tcga_info** (object) - An object containing information about the TCGA data, including XenaHub object and DataInfo.

#### Response Example
```json
{
  "Xena": { ... },
  "DataInfo": [ ... ]
}
```
```

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

### XenaBrowse - Open Dataset in Web Browser

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Opens the UCSC Xena web page for a specific dataset or cohort in your default browser.

```APIDOC
## XenaBrowse - Open Dataset in Web Browser

### Description
Opens the UCSC Xena web page for a specific dataset or cohort in your default browser.

### Method
GET

### Endpoint
/api/v1/XenaBrowse

### Parameters
#### Query Parameters
- **data** (object) - Required - A XenaHub object or a list of datasets to browse.
- **type** (string) - Optional - The type of page to open ('dataset' or 'cohort'). Defaults to 'dataset'.
- **multiple** (boolean) - Optional - If TRUE, allows browsing multiple datasets. Defaults to FALSE.

### Request Example
```json
{
  "data": {
    "host": "https://tcga.xenahubs.net",
    "datasets": ["clinical", "LUAD"]
  },
  "type": "dataset",
  "multiple": false
}
```
```

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

### Update Xena Dataset Information

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Retrieves the latest dataset information from UCSC Xena hubs. Can optionally save this information locally. Use `saveTolocal = FALSE` to only retrieve.

```r
library(UCSCXenaTools)

# Update dataset information (not saved locally)
new_data <- XenaDataUpdate(saveTolocal = FALSE)
#> => Obtaining info from UCSC Xena hubs...
#> ==> Searching cohorts for host https://ucscpublic.xenahubs.net...
#> ===> #XX cohorts found.
#> ...
#> => Done.

# Update and save to package data directory (requires write permission)
XenaDataUpdate(saveTolocal = TRUE)
```

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

### Direct TCGA Data Download

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Provides direct download of TCGA data by specifying project, data type, and file type explicitly. Includes functions to check available options and existing data for a project.

```r
library(UCSCXenaTools)

# Check available options
availTCGA("all")
#> $ProjectID
#> [1] "LAML" "ACC" "CHOL" "BLCA" "BRCA" ...
#> $DataType
#> [1] "Gene Level Copy Number" "Copy Number Segments" ...
#> $FileType
#> [1] "Gistic2" "Gistic2 thresholded" ...

# Download specific data type
downloadTCGA(
  project = "UVM",
  data_type = "Gene Expression RNASeq",
  file_type = "IlluminaHiSeq RNASeqV2",
  destdir = "~/tcga_data/"
)

# Check what data exists for a project
showTCGA("LUAD")
#>   ProjectID                    DataType                      FileType
#> 1      LUAD         Gene Level Copy Number                      Gistic2
#> 2      LUAD         Gene Level Copy Number           Gistic2 thresholded
#> ...

```

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

### Simplified TCGA Data Download

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Provides a simplified interface for downloading common TCGA datasets by project ID and data type. Can fetch data information without downloading. Supports multiple RNA-seq normalizations.

```r
library(UCSCXenaTools)

# Get data information without downloading
tcga_info <- getTCGAdata(
  project = "LUAD",
  clinical = TRUE,
  mRNASeq = TRUE,
  mRNASeqType = "normalized",
  Methylation = TRUE,
  MethylationType = "450K",
  GeneMutation = TRUE,
  download = FALSE
)

# View the XenaHub object and data info
tcga_info$Xena
tcga_info$DataInfo

# Download TCGA data for multiple projects
getTCGAdata(
  project = c("LUAD", "LUSC"),
  clinical = TRUE,
  mRNASeq = TRUE,
  RPPAArray = TRUE,
  GeneMutation = TRUE,
  download = TRUE,
  destdir = "~/tcga_data/"
)

# Download with all RNA-seq normalizations
getTCGAdata(
  project = "GBM",
  mRNASeq = TRUE,
  mRNASeqType = c("normalized", "pancan normalized", "percentile"),
  download = TRUE
)
```

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

### XenaDataUpdate - Update Dataset Information

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Retrieves the latest dataset information from all UCSC Xena hubs and optionally saves it locally.

```APIDOC
## XenaDataUpdate - Update Dataset Information

### Description
Retrieves the latest dataset information from all UCSC Xena hubs and optionally saves it locally.

### Method
GET

### Endpoint
/api/v1/XenaDataUpdate

### Parameters
#### Query Parameters
- **saveTolocal** (boolean) - Optional - If TRUE, saves the updated dataset information locally. Defaults to FALSE.

### Response
#### Success Response (200)
- **new_data** (object) - An object containing the latest dataset information from Xena hubs.

#### Response Example
```json
{
  "host1": {
    "cohort1": {
      "dataset1": { ... },
      "dataset2": { ... }
    }
  }
}
```
```

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

### Filter XenaHub Datasets

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Filters a XenaHub object to select specific cohorts or datasets using regular expressions. Multiple filters can be chained using the pipe operator.

```r
library(UCSCXenaTools)

# Filter TCGA hub for clinical datasets
xe <- XenaGenerate(subset = XenaHostNames == "tcgaHub")

# Filter for clinical data
xe_clinical <- XenaFilter(xe, filterDatasets = "clinical")
datasets(xe_clinical)

# Chain multiple filters - get clinical data for specific cancer types
XenaGenerate(subset = XenaHostNames == "tcgaHub") %>%
  XenaFilter(filterDatasets = "clinical") %>%
  XenaFilter(filterDatasets = "LUAD|LUSC|LUNG") -> df_todo

df_todo
#> class: XenaHub
#> hosts():
#>   https://tcga.xenahubs.net
#> cohorts() (3 total):
#>   TCGA Lung Cancer (LUNG)
#>   TCGA Lung Adenocarcinoma (LUAD)
#>   TCGA Lung Squamous Cell Carcinoma (LUSC)
#> datasets() (3 total):
#>   TCGA.LUNG.sampleMap/LUNG_clinicalMatrix
#>   TCGA.LUAD.sampleMap/LUAD_clinicalMatrix
#>   TCGA.LUSC.sampleMap/LUSC_clinicalMatrix
```

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

### Filter Datasets for Specific Hubs and Types

Source: https://github.com/ropensci/ucscxenatools/blob/master/README.md

Select datasets from the 'tcgaHub' by filtering for 'clinical' data and then further refining the selection to include datasets related to 'LUAD', 'LUSC', or 'LUNG'. This demonstrates the use of regular expressions for flexible filtering.

```r
# The options in XenaFilter function support Regular Expression
XenaGenerate(subset = XenaHostNames=="tcgaHub") %>%
  XenaFilter(filterDatasets = "clinical") %>%
  XenaFilter(filterDatasets = "LUAD|LUSC|LUNG") -> df_todo

df_todo
#> class: XenaHub 
#> hosts():
#>   https://tcga.xenahubs.net
#> cohorts() (3 total):
#>   TCGA Lung Cancer (LUNG)
#>   TCGA Lung Adenocarcinoma (LUAD)
#>   TCGA Lung Squamous Cell Carcinoma (LUSC)
#> datasets() (3 total):
#>   TCGA.LUNG.sampleMap/LUNG_clinicalMatrix
#>   TCGA.LUAD.sampleMap/LUAD_clinicalMatrix
#>   TCGA.LUSC.sampleMap/LUSC_clinicalMatrix
```

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

### Query Gene Expression Values with fetch_dense_values

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Fetches expression values for specific genes and samples directly from UCSC Xena without downloading entire datasets. Supports gene symbol queries via ProbeMap.

```r
library(UCSCXenaTools)

# Define host and dataset
host <- "https://toil.xenahubs.net"
dataset <- "tcga_RSEM_gene_tpm"

# Define samples and genes
samples <- c("TCGA-02-0047-01", "TCGA-02-0055-01", "TCGA-02-2483-01", "TCGA-02-2485-01")
probes <- c("ENSG00000282740.1", "ENSG00000000005.5", "ENSG00000000419.12")
genes <- c("TP53", "RB1", "PIK3CA")

# Fetch by probe IDs
expr_matrix <- fetch_dense_values(
  host = host,
  dataset = dataset,
  identifiers = probes,
  samples = samples,
  check = FALSE
)
```

```r
# Fetch by gene symbols using ProbeMap
expr_genes <- fetch_dense_values(
  host = host,
  dataset = dataset,
  identifiers = genes,
  samples = samples,
  check = FALSE,
  use_probeMap = TRUE
)
#> -> Checking if the dataset has probeMap...
#> -> Done. ProbeMap is found.
#> -> Query done.

# Result is a matrix with genes as rows and samples as columns
expr_genes
#>          TCGA-02-0047-01 TCGA-02-0055-01 TCGA-02-2483-01 TCGA-02-2485-01
#> TP53           10.234          9.876          10.123          9.987
#> RB1             8.567          8.234          8.901          8.456
#> PIK3CA          7.890          7.654          7.321          7.789
```

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

### Check for Probe Mapping in Dataset

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Checks if a dataset has an associated ProbeMap for converting between probe IDs and gene symbols. Can also return the ProbeMap URL.

```r
library(UCSCXenaTools)

host <- "https://toil.xenahubs.net"
dataset <- "tcga_RSEM_gene_tpm"

# Check if ProbeMap exists
has_probeMap(host, dataset)
#> [1] TRUE

# Get the ProbeMap URL
probeMap_url <- has_probeMap(host, dataset, return_url = TRUE)
probeMap_url
#> [1] "https://toil.xenahubs.net/download/probeMap/gencode.v23.annotation.gene.probemap"
```

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

### has_probeMap - Check for Probe Mapping

Source: https://context7.com/ropensci/ucscxenatools/llms.txt

Checks if a dataset has an associated ProbeMap for converting between probe IDs and gene symbols.

```APIDOC
## has_probeMap - Check for Probe Mapping

### Description
Checks if a dataset has an associated ProbeMap for converting between probe IDs and gene symbols.

### Method
GET

### Endpoint
/api/v1/hasProbeMap

### Parameters
#### Query Parameters
- **host** (string) - Required - The base URL of the Xena hub.
- **dataset** (string) - Required - The identifier of the dataset.
- **return_url** (boolean) - Optional - If TRUE, returns the URL of the ProbeMap.

### Response
#### Success Response (200)
- **result** (boolean or string) - TRUE if ProbeMap exists, FALSE otherwise. If `return_url` is TRUE, returns the ProbeMap URL.

#### Response Example (Boolean)
```json
true
```

#### Response Example (URL)
```json
"https://toil.xenahubs.net/download/probeMap/gencode.v23.annotation.gene.probemap"
```
```

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