R/fetchComponents.R

In hyginn/BCB420.2019.ESA: Exploratory Systems Analysis Tools

# fetchComponents.R

#' \code{fetchComponents} get all gene symbols in a system.
#'
#' \code{fetchComponents} is deprecated. Use \code{SyDBgetSysSymbols()} instead.
#'
#' @param sys (character)  Name of a system
#'
#' @return (character) a vector of HGNC symbols
#' @examples
#' \dontrun{
#' fetchComponents("PHALY")  # all PHALY system proteins
#' }
#' @export

fetchComponents <- function(sys) {
  # returns a fixed set of symbols.
  # Function stub for development purposes only.

  message("Note: fetchComponents(...) is deprecated.",
          "Use SyDBgetSysSymbols(<database>, <system code>) instead.",
          sep = "\n")

    if (sys == "PHALY") {
    s <- c("AMBRA1", "ATG14", "ATP2A1", "ATP2A2", "ATP2A3", "BECN1", "BECN2",
           "BIRC6", "BLOC1S1", "BLOC1S2", "BORCS5", "BORCS6", "BORCS7",
           "BORCS8", "CACNA1A", "CALCOCO2", "CTTN", "DCTN1", "EPG5", "GABARAP",
           "GABARAPL1", "GABARAPL2", "HDAC6", "HSPB8", "INPP5E", "IRGM",
           "KXD1", "LAMP1", "LAMP2", "LAMP3", "LAMP5", "MAP1LC3A", "MAP1LC3B",
           "MAP1LC3C", "MGRN1", "MYO1C", "MYO6", "NAPA", "NSF", "OPTN",
           "OSBPL1A", "PI4K2A", "PIK3C3", "PLEKHM1", "PSEN1", "RAB20", "RAB21",
           "RAB29", "RAB34", "RAB39A", "RAB7A", "RAB7B", "RPTOR", "RUBCN",
           "RUBCNL", "SNAP29", "SNAP47", "SNAPIN", "SPG11", "STX17", "STX6",
           "SYT7", "TARDBP", "TFEB", "TGM2", "TIFA", "TMEM175", "TOM1",
           "TPCN1", "TPCN2", "TPPP", "TXNIP", "UVRAG", "VAMP3", "VAMP7",
           "VAMP8", "VAPA", "VPS11", "VPS16", "VPS18", "VPS33A", "VPS39",
           "VPS41", "VTI1B", "YKT6")
  } else {
    s <- ""
  }

  return(s)
}

# [END]