queryFirebrowseData {psichomics} | R Documentation |
Query the Firebrowse API for TCGA data
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 )
format |
Character: response format as |
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) |
Response from the Firebrowse API (it needs to be parsed)
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))