queryFirebrowseData {psichomics} | R Documentation

## Query the Firebrowse web API for TCGA data

### Description

Query the Firebrowse web 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` (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)

### Value

Response from the Firebrowse web API (it needs to be parsed)

### Examples

    cohort <- psichomics:::getFirebrowseCohorts()[1]
    psichomics:::queryFirebrowseData(cohort = cohort, data_type = "mRNASeq")

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

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

[Package psichomics version 1.8.2 Index]