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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: 2024-03-25 07:26
#>   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: 2024-03-25 07:26
#>   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",
#> ...