R/mappingDBs.R

In soderling-lab/geneLists: tools for mapping gene identifiers and a collection of gene lists in a universal format

#' mappingDBs()
#'
#' Returns a list of annotation databases.
#' Note: requires the organism specific database to be installed. For example,
#' for mapping mouse genes, you should have installed "org.Mm.eg.db" with
#' BiocManager.
#'
#' @author Tyler W Bradshaw, \email{twesleyb10@gmail.com}
#'
#' @export mappingDBs 

mappingDBs <- function() {
  annotationDBs <- list(
    Anopheles_gambia = list(
      taxid = 7165, database = "org.Ag.eg.db",
      alias = "anopheles"
    ),
    Arabidopsis_thaliana = list(
      taxid = 7302, database = "org.At.tair.db",
      alias = "arabidopsis"
    ),
    Bos_taurus = list(
      taxid = 9913, database = "org.Bt.eg.db",
      alias = "bovine"
    ),
    Caenorhabditis_elegans = list(
      taxid = 6239, database = "org.Ce.eg.db",
      alias = "worm"
    ),
    Canis_familiaris = list(
      taxid = 9615, database = "org.Cf.eg.db",
      alias = "dog"
    ),
    Drosophila_melanogaster = list(
      taxid = 7227, database = "org.Dm.eg.db",
      alias = "fly"
    ),
    Danio_rerio = list(
      taxid = 7955, database = "org.Dr.eg.db",
      alias = "zebrafish"
    ),
    Escherichia_coliSakai = list(
      taxid = 386585, database = "org.EcSakai.eg.db",
      alias = "ecoli-sakai"
    ),
    Gallus_gallus = list(
      taxid = 9031, database = "org.Gg.eg.db",
      alias = "chicken"
    ),
    Homo_sapiens = list(
      taxid = 9606, database = "org.Hs.eg.db",
      alias = "human"
    ),
    Mus_musculus = list(
      taxid = 10090, database = "org.Mm.eg.db",
      alias = "mouse"
    ),
    Macaca_mulatta = list(
      taxid = 9544, database = "org.Mmu.eg.db",
      alias = "macaque"
    ),
    Plasmodium_falciparum = list(
      taxid = 5833, database = "org.Pf.plasmo.db",
      alias = "malaria"
    ),
    Pan_troglodytes = list(
      taxid = 9598, database = "org.Pt.eg.db",
      alias = "chimp"
    ),
    Rattus_norvegicus = list(
      taxid = 10116, database = "org.Rn.eg.db",
      alias = "rat"
    ),
    Saccharomyces_cerevisiae = list(
      taxid = 4932, database = "org.Sc.sgd.db",
      alias = "yeast"
    ),
    Sus_scrofa = list(
      taxid = 9823, database = "org.Ss.eg.db",
      alias = "pig"
    ),
    Xenopus_laevis = list(
      taxid = 8355, database = "org.Xl.eg.db",
      alias = "frog"
    )
  )
  return(annotationDBs)
}