loadTCGAdata {psichomics} | R Documentation

## Download and process TCGA data

### Description

TCGA data obtained via FireBrowse

### Usage

    loadTCGAdata(
      folder = getDownloadsFolder(),
      data = c("clinical", "junction_quantification", "RSEM_genes"),
      exclude = c(".aux.", ".mage-tab.", "MANIFEST.txt"),
      ...,
      download = TRUE
    )

### Arguments

`folder` | Character: directory to store the downloaded archives (by default, saves to `getDownloadsFolder()`)
`data` | Character: data to load (see `getTCGAdataTypes()`)
`exclude` | Character: files and folders to exclude from downloading and from loading into R (by default, exclude files containing `.aux.`, `.mage-tab.` and `MANIFEST.TXT`)
`...` | Arguments passed on to `queryFirebrowseData` `date` Character: dates of the data retrieval by FireBrowse (by default, it uses the most recent data available) `cohort` Character: abbreviation of the cohorts (by default, returns data for all cohorts) `data_type` Character: data types (optional) `tool` Character: data produced by the selected FireBrowse tools (optional) `platform` Character: data generation platforms (optional) `center` Character: data generation centres (optional) `level` Integer: data levels (optional) `protocol` Character: sample characterization protocols (optional) `page` Integer: page of the results to return (optional) `page_size` Integer: number of records per page of results (optional) `sort_by` String: column used to sort the data (by default, sort by cohort)
`download` | Boolean: download missing files

### Value

A list with the loaded data, unless required files are unavailable and `download = FALSE` (if so, it returns the URL of files to download)

### See Also

Other functions associated with TCGA data retrieval: `getDownloadsFolder()`, `getTCGAdataTypes()`, `isFirebrowseUp()`, `parseTCGAsampleTypes()`

Other functions to load data: `loadGtexData()`, `loadLocalFiles()`, `loadSRAproject()`

### Examples

    getTCGAcohorts()
    getTCGAdataTypes()
    ## Not run:
    loadTCGAdata(cohort = "ACC", data_type = "Clinical")

    ## End(Not run)

[Package psichomics version 1.20.2 Index]