queryFirebrowseData {psichomics} | R Documentation

## Query the Firebrowse API for TCGA data

### Description

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")

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

    psichomics:::queryFirebrowseData(date = dates[2], cohort = names(cohort))

[Package psichomics version 1.16.0 Index]