queryFirebrowseData: Query the Firebrowse API for TCGA data

In psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

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))

psichomics documentation built on Nov. 8, 2020, 5:44 p.m.