#' @title Get MMRF-COMPASS Project Summary from GDC
#' @export
#' @examples
#' \dontrun{
#' getProjectSummary()
#' }
MMRF_getProjectSummary <- function(){
project<-"MMRF-COMMPASS"
baseURL <- "https://api.gdc.cancer.gov/projects/"
url <- paste0(baseURL, project,"?expand=summary,summary.data_categories&pretty=true")
summary<-fromJSON(url,simplifyDataFrame = TRUE)$data$summary
return(summary)
}
#' @title Get Number of cases of MMRF-COMMPASS project from GDC
#' @param data.category A GDC project data category
#' @export
#' @examples
#' \dontrun{
#' getNbCases("Clinical")
#' }
MMRF_getNbCases <- function(data.category){
summary <- MMRF_getProjectSummary()
if(data.category %in% summary$data_categories$data_category){
summary <- getProjectSummary()$data_categories
nb <- summary[summary$data_category == data.category,"case_count"]
} else {
nb <- summary$case_count
}
return(nb)
}
#' @title Get Number of files in MMRF-COMMPASS project
#' @param data.category A GDC project data category
#' @param legacy Select between Harmonized or Legacy database
#' @export
#' @examples
#' \dontrun{
#' getNbFiles("Clinical")
#' }
MMRF_getNbFiles <- function(data.category){
summary <- getProjectSummary()
if(data.category %in% summary$data_categories$data_category){
summary <- getProjectSummary()$data_categories
nb <- summary[summary$data_category == data.category,"file_count"]
} else {
nb <- summary$file_count
}
return(nb)
}
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