R/downloadPc.R

In BioPAX/paxtoolsr: Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

#' #' Download Pathway Commons data (DEPRECATED)
#' #' 
#' #' Download Pathway Commons data in various formats
#' #' 
#' #' @param format a string describing the format to be downloaded; 
#' #'   currently, only the Extended Simple Interaction Format (SIF) "SIFNX" and 
#' #'   Gene Set Enrichment Analysis "GMT" formats for the entire Pathway Commons 
#' #'   database are supported. 
#' #' @param verbose a boolean debugging information
#' #' @return a named list with named pathways, each entry contains a vector of gene 
#' #'   symbols (for GMT) or a list with two data.frames (for SIFNX): 
#' #'   \itemize{ 
#' #'     \item edges Network edges with the following columns: 
#' #'       PARTICIPANT_A: Edge (interaction) participant, 
#' #'       INTERACTION_TYPE: Interaction type (see details), 
#' #'       PARTICIPANT_B: Edge (interaction) participant, 
#' #'       INTERACTION_DATA_SOURCE: Semi-colon delimited list of database sources 
#' #'         of the interaction, 
#' #'       INTERACTION_PUBMED_ID: Semi-colon delimited list of NCBI Pubmed IDs 
#' #'         that give evidence for the interaction 
#' #'     \item nodes Node information: 
#' #'       PARTICIPANT: Interaction participant,
#' #'       PARTICIPANT_TYPE: BioPAX class (see details),
#' #'       PARTICIPANT_NAME: Display name for the participant, 
#' #'       UNIFICATION_XREF: A UnificationXref defines a reference to an entity 
#' #'         in an external resource that has the same biological identity as 
#' #'         the referring entity, 
#' #'       RELATIONSHIP_XREF: An RelationshipXref defines a reference to an entity
#' #'         in an external resource that does not have the same biological 
#' #'         identity as the referring entity.
#' #'   }
#' #'  
#' #' @details 
#' #' 
#' #' Use \code{\link{downloadPc2}}
#' #' 
#' #' @examples 
#' #' \dontrun{
#' #' downloadPc(format="GMT") 
#' #' }
#' #' 
#' #' @concept paxtoolsr
#' #' @seealso \code{\link{downloadPc2}}
#' #' @export 
#' downloadPc <- function(format=c("SIFNX", "GMT"), verbose=FALSE) {    
#'     if(format == "SIFNX") {
#'         orgFile <- tempfile("sifnx", fileext=".gz")
#'         
#'         url <- paste0(getPcUrl(), "downloads/Pathway%20Commons.", getOption("pc.version"), 
#'                       ".All.EXTENDED_BINARY_SIF.hgnc.sif.gz ")
#'         
#'         if(verbose) {
#'             cat("URL: ", url, "\n")
#'         }
#'         
#'         download.file(url, orgFile)
#'         
#'         #con <- gzcon(file(orgFile, "r"))
#'         results <- readSifnx(orgFile)
#'     }
#'     
#'     if(format == "BIOPAX") {
#'     }  
#'     
#'     if(format == "GMT") {
#'         file <- tempfile("gmt", fileext = ".gz")
#'         url <- paste0(getPcUrl(), "downloads/Pathway%20Commons.", getOption("pc.version"), 
#'                       ".All.GSEA.hgnc.gmt.gz")
#'         
#'         if(verbose) {
#'             cat("URL: ", url, "\n")
#'         }
#'         
#'         download.file(url, file)
#'         
#'         results <- readGmt(gzfile(file))
#'     }
#'     
#'     return(results)       
#' }