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 = getDownloadsFolder(), 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 1.10.1 Index]