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 1.10.2 Index]