comparison GO-enrich.R @ 8:b29255864039 draft

planemo upload commit b636a89be85c5695c234abcf4960a731549ddd57-dirty

7:4609346d8108

  # Parse arguments
  parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
  argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
  args <- as.list(as.character(argsDF$V2))
  names(args) <- argsDF$V1
  plot = unlist(strsplit(args$plot,","))
  go_represent=str2bool(args$go_represent)
  go_enrich=str2bool(args$go_enrich)
  
  #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda")
  #load("/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda")
  
  suppressMessages(library(args$species, character.only = TRUE, quietly = TRUE))
  
  # Extract OrgDb
  if (args$species=="org.Hs.eg.db") {

        }
        universe_header = str2bool(args$uheader)
        # Get file content
        universe_file = read_file(universe_filename, universe_header)
        # Extract Protein IDs list
        universe <- sapply(universe_file[,universe_ncol], function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE)
      }
      universe_id_type = args$universe_id_type
      ##to initialize
      if (universe_id_type=="Uniprot" & any(check_ids(universe,"uniprot"))) {
        idFrom<-"UNIPROT"

8:b29255864039

  # Parse arguments
  parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
  argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
  args <- as.list(as.character(argsDF$V2))
  names(args) <- argsDF$V1
  
  #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda")
  #load("/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda")
  
  plot = unlist(strsplit(args$plot,","))
  go_represent=str2bool(args$go_represent)
  go_enrich=str2bool(args$go_enrich)
  
  suppressMessages(library(args$species, character.only = TRUE, quietly = TRUE))
  
  # Extract OrgDb
  if (args$species=="org.Hs.eg.db") {

        }
        universe_header = str2bool(args$uheader)
        # Get file content
        universe_file = read_file(universe_filename, universe_header)
        # Extract Protein IDs list
        universe <- unlist(sapply(universe_file[,universe_ncol], function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE))
      }
      universe_id_type = args$universe_id_type
      ##to initialize
      if (universe_id_type=="Uniprot" & any(check_ids(universe,"uniprot"))) {
        idFrom<-"UNIPROT"