R/enhance_build_Anno.R

In xiayh17/RNAseqStat: A Pipeline to Process RNAseq Data

#' @importFrom kit fduplicated
enhance_build_Anno <- function(path2gene, path2name) {
  if (!exists(".Anno_clusterProfiler_Env", envir = .GlobalEnv)) {
    pos <- 1
    envir <- as.environment(pos)
    assign(".Anno_clusterProfiler_Env", new.env(), envir = envir)
  }
  Anno_clusterProfiler_Env <- get(".Anno_clusterProfiler_Env", envir= .GlobalEnv)

  if(class(path2gene[[2]]) == 'list') {
    ## to compatible with tibble
    path2gene <- cbind(rep(path2gene[[1]],
                           times = vapply(path2gene[[2]], length, numeric(1))),
                       unlist(path2gene[[2]]))
  }

  path2gene <- as.data.frame(path2gene)
  path2gene <- path2gene[!is.na(path2gene[,1]), ]
  path2gene <- path2gene[!is.na(path2gene[,2]), ]
  # path2gene <- unique(path2gene)
  path2gene <- path2gene[!kit::fduplicated(path2gene),]

  PATHID2EXTID <- split(as.character(path2gene[,2]), as.character(path2gene[,1]))
  EXTID2PATHID <- split(as.character(path2gene[,1]), as.character(path2gene[,2]))

  assign("PATHID2EXTID", PATHID2EXTID, envir = Anno_clusterProfiler_Env)
  assign("EXTID2PATHID", EXTID2PATHID, envir = Anno_clusterProfiler_Env)

  if ( missing(path2name) || is.null(path2name) || all(is.na(path2name))) {
    assign("PATHID2NAME", NULL, envir = Anno_clusterProfiler_Env)
  } else {
    path2name <- as.data.frame(path2name)
    path2name <- path2name[!is.na(path2name[,1]), ]
    path2name <- path2name[!is.na(path2name[,2]), ]
    # path2name <- unique(path2name)
    path2name <- path2name[!kit::fduplicated(path2name),]
    PATH2NAME <- as.character(path2name[,2])
    names(PATH2NAME) <- as.character(path2name[,1])
    assign("PATHID2NAME", PATH2NAME, envir = Anno_clusterProfiler_Env)
  }
  return(Anno_clusterProfiler_Env)
}