R/checkTCGA.R

In RTCGA/RTCGA: The Cancer Genome Atlas Data Integration

## RTCGA package for R
#' @title Information About Datasets from TCGA Project
#'
#' @description The \code{checkTCGA} function let's to check
#'  
#' \itemize{
#'      \item \code{DataSets}: TCGA datasets' names for current release date and cohort.
#'      \item \code{Dates}: TCGA datasets' dates of release.
#'  }
#'   
#' 
#' @details 
#' \itemize{
#'      \item If \code{what='DataSets'} enables to check TCGA datasets' names for current release date and cohort.
#'      \item If \code{what='Dates'} enables to check dates of TCGA datasets' releases.
#'      }
#' @return 
#' \itemize{
#'      \item If \code{what='DataSets'} a data.frame of available datasets' names (to pass to the \link{downloadTCGA} function) and sizes.
#'      \item If \code{what='Dates'} a vector of available dates to pass to the \link{downloadTCGA} function.
#'      }
#' @param what One of \code{DataSets} or \code{Dates}.     
#' @param cancerType A character of length 1 containing abbreviation (Cohort code - \href{https://gdac.broadinstitute.org/}{https://gdac.broadinstitute.org/})
#'  of types of cancers to check for.
#' @param date A \code{NULL} or character specifying from which date informations should be checked.
#' By default (\code{date = NULL}) the newest available date is used. All available dates can be checked on 
#' \href{https://gdac.broadinstitute.org/runs/}{https://gdac.broadinstitute.org/runs/} or by using \code{checkTCGA('Dates')} 
#' function. Required format \code{'YYYY-MM-DD'}.
#' 
#' 
#' @section Issues:
#' 
#' If you have any problems, issues or think that something is missing or is not
#' clear please post an issue on 
#' \href{https://github.com/RTCGA/RTCGA/issues}{https://github.com/RTCGA/RTCGA/issues}.
#' 
#' @author 
#' Marcin Kosinski, \email{m.p.kosinski@@gmail.com}
#' 
#' @seealso 
#' 
#' \pkg{RTCGA} website \href{https://rtcga.github.io/RTCGA/}{https://rtcga.github.io/RTCGA/}.
#' 
#' @examples
#' 
#' ############################# 
#' 
#' # names for current release date and cohort
#' checkTCGA('DataSets', 'BRCA')
#' \dontrun{
#' checkTCGA('DataSets', 'OV', tail(checkTCGA('Dates'))[3])
#' #checkTCGA('DataSets', 'OV', checkTCGA('Dates')[5]) # error
#' }
#' # dates of TCGA datasets' releases.
#' checkTCGA('Dates')
#' 
#' ############################# 
#' \dontrun{
#' # TCGA datasets' names availability for 
#' # current release date and cancer type.
#' 
#' releaseDate <- '2015-08-21'
#' cancerTypes <- c('OV', 'BRCA')
#' 
#' cancerTypes %>% sapply(function(element){
#'   grep(x = checkTCGA('DataSets', element, releaseDate)[, 1], 
#'       pattern = 'humanmethylation450', value = TRUE) %>%
#'        as.vector()
#'        })
#'        
#' }
#' @family RTCGA
#' @aliases checkTCGA
#' @rdname checkTCGA
#' @export
checkTCGA <- function(what, cancerType, date = NULL) {
	assert_that(is.character(what) & length(what) == 1)
	assert_that(is.null(date) || (is.character(cancerType) & (length(cancerType) == 1)))
	assert_that(is.null(date) || (is.character(date) & (length(date) == 1)))
	
	if (what == "DataSets") {
		return(availableDataSets(cancerType, date = date))
	}
	if (what == "Dates") {
		return(availableDates())
	}
}

# Misc function
availableDataSets <- function(cancerType, date = NULL) {
	
	assertthat::assert_that(is.character(cancerType) & (length(cancerType) == 1))
	assertthat::assert_that(is.null(date) || (is.character(date) & (length(date) == 1)))
	
	# ensure which date was specified
	lastReleaseDate <- whichDateToUse(date = date)  #downloadTCGA.r
	
	# get index of page containing datasets fot this date of release and Cohort Code
	filesParentURL <- parentURL(lastReleaseDate, element = cancerType)  #downloadTCGA.r
	
	
	url <- getURL(filesParentURL, .opts = list(ssl.verifypeer = FALSE))
	# get content of index page
	readHTMLTable(url)[[1]][-c(1:2), c(2,4)] -> check
	check[!grepl('md5', check[,1]) , ] -> check
	check[!grepl('aux', check[,1]) , ] -> check
	check[!grepl('mage-tab', check[,1]) , ] -> check
	check[, 1] <- gsub("gdac.broadinstitute.org_", "", check[, 1])
	na.omit(check) -> check
	rownames(check) <- 1:nrow(check)
	return(check[, c(2,1)])
	
	
	
}


# Misc function
availableDates <- function() {
	
	if (!exists(x = ".availableDates3", envir = .RTCGAEnv)) {
		# happens only once
		readLines("https://gdac.broadinstitute.org/runs/") %>% assign(x = ".gdacContent", value = ., envir = .RTCGAEnv)
		
		get(".gdacContent", envir = .RTCGAEnv) %>% grep(pattern = "stddata__20", value = TRUE) %>% gsub(pattern = "(<[^>]+>)| |/", replacement = "") %>% 
			substring(first = 10, last = 19) %>% assign(x = ".availableDates", value = ., envir = .RTCGAEnv)
		
		get(".availableDates", envir = .RTCGAEnv) %>% gsub(pattern = "^[^0-9]{10}", replacement = "") %>% gsub(pattern = "_", replacement = "-", 
																																																					 fixed = TRUE) %>% assign(x = ".availableDates2", value = ., envir = .RTCGAEnv)
		
		############################################ 
		
		xml2::read_html("https://gdac.broadinstitute.org/runs/stddata__latest/") %>% html_nodes("h3") %>% html_text() %>%
			substring(first=1, last=10) %>% gsub(pattern = "_", replacement = "-", fixed = TRUE) %>% 
			assign(x = ".lastWorkingDate", value = ., envir = .RTCGAEnv)
		get(x = ".availableDates2", envir = .RTCGAEnv)[1:grep(get(x = ".lastWorkingDate", envir = .RTCGAEnv), 
																													get(x = ".availableDates2", envir = .RTCGAEnv) )] %>%
			assign(x=".availableDates3", value = ., envir = .RTCGAEnv)
	}
	get(x=".availableDates3", envir = .RTCGAEnv)
}