Query the FireBrowse API for TCGA data

Usage

queryFirebrowseData(
  format = "json",
  date = NULL,
  cohort = NULL,
  data_type = NULL,
  tool = NULL,
  platform = NULL,
  center = NULL,
  level = NULL,
  protocol = NULL,
  page = NULL,
  page_size = NULL,
  sort_by = NULL
)

Arguments

format: Character: response format as JSON, 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 (optional)
sort_by: String: column used to sort the data (by default, sort by cohort)

Value

Response from the FireBrowse API (it needs to be parsed)

Examples

cohort <- getTCGAcohorts()[1]
psichomics:::queryFirebrowseData(cohort = names(cohort),
                                 data_type = "mRNASeq")
#> Response [http://firebrowse.org/api/v1/Archives/StandardData?format=json&date=2016_01_28&cohort=ACC&data_type=mRNASeq]
#>   Date: 2024-11-18 07:41
#>   Status: 200
#>   Content-Type: application/json
#>   Size: 12.1 kB
#> {
#>   "StandardData": [
#>     {
#>       "active": true,
#>       "center": "unc.edu",
#>       "cohort": "ACC",
#>       "data_type": "mRNASeq",
#>       "date": "Thu, 28 Jan 2016 00:00:00 GMT",
#>       "filesize": 16560553,
#>       "level": 3,
#> ...

# Querying for data from a specific date
dates <- getTCGAdates()
dates <- format(dates, psichomics:::getFirebrowseDateFormat()$query)

psichomics:::queryFirebrowseData(date = dates[2], cohort = names(cohort))
#> Response [http://firebrowse.org/api/v1/Archives/StandardData?format=json&date=2015_11_01&cohort=ACC]
#>   Date: 2024-11-18 07:41
#>   Status: 200
#>   Content-Type: application/json
#>   Size: 37.2 kB
#> {
#>   "StandardData": [
#>     {
#>       "active": true,
#>       "center": "unc.edu",
#>       "cohort": "ACC",
#>       "data_type": "mRNASeq",
#>       "date": "Sun, 01 Nov 2015 00:00:00 GMT",
#>       "level": 3,
#>       "platform": "illuminahiseq_rnaseqv2",
#> ...