loadFirebrowseData {psichomics} | R Documentation

## Downloads and processes data from the Firebrowse web API and loads it into R

### Description

Downloads and processes data from the Firebrowse web API and loads it into R

### Usage

    loadFirebrowseData(folder = NULL, data = NULL, exclude = c(".aux.",
      ".mage-tab.", "MANIFEST.txt"), ..., download = TRUE)

    loadFirehoseData(folder = NULL, data = NULL, exclude = c(".aux.",
      ".mage-tab.", "MANIFEST.txt"), ..., download = TRUE)

    loadTCGAdata(folder = NULL, data = NULL, exclude = c(".aux.",
      ".mage-tab.", "MANIFEST.txt"), ..., download = TRUE)

### Arguments

`folder` | Character: directory to store the downloaded archives (by default, it saves in the user's "Downloads" folder)
`data` | Character: data to load
`exclude` | Character: files and folders to exclude from downloading and from loading into R (by default, it excludes `.aux.`, `.mage-tab.` and `MANIFEST.TXT` files)
`...` | Arguments passed on to `queryFirebrowseData` format Character: response format as `JSON` (default), `CSV` or `TSV` 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; max is 2000 (optional) sort_by String: column used to sort the data (by default, it sorts by cohort)
`download` | Boolean: download missing files through the function `download.file` (TRUE by default)

### Value

URL of missing files ("missing" class) if files need to be downloaded and if the argument `download` is `FALSE`; else, a list with loaded data

### Examples

    ## Not run:
    loadFirebrowseData(cohort = "ACC", data_type = "Clinical")

    ## End(Not run)

[Package psichomics version 1.6.2 Index]