R/ZZZ.R

In aiminy/PathwaySplice: An R Package for Adjusting Bias in Gene Set Enrichment Analysis

#' Title
#'
#' @param libname
#' @param pkgname
#'
#' @return
#' @export
#'
#' @examples

.onAttach <- function(libname, pkgname) {
    if (.Platform$OS.type == "windows" && .Platform$GUI == "Rgui") {
        base::winMenuAddItem("Vignettes", "PathwaySplice", "shell.exec(system.file(\"doc\",\"PathwaySplice.pdf\",package=\"PathwaySplice\"))")
    }
}

# These two variables are required for automatic fetching of
# categories to function.  Their purpose is to take the UCSC
# genome and gene ID values given when looking up length data
# and convert them to the names used for the same organism
# and gene identifier in the organism packages.

# Mappings that are primarily required by getgo, the purpose
# of this is to convert the UCSC genome IDs, to the
# bioconductor organism names, e.g. 'mm'->'org.Mm.'
.ORG_PACKAGES = paste("org.", c("Ag.eg", "At.tair", "Bt.eg", 
    "Ce.eg", "Cf.eg", "Dm.eg", "Dr.eg", "EcK12.eg", "EcSakai.eg", 
    "Gg.eg", "Hs.eg", "Mm.eg", "Mmu.eg", "Pf.plasmo", "Pt.eg", 
    "Rn.eg", "Sc.sgd", "Ss.eg", "Xl.eg"), sep = "")
names(.ORG_PACKAGES) = c("anoGam", "Arabidopsis", "bosTau", "ce", 
    "canFam", "dm", "danRer", "E. coli K12", "E. coli Sakai", 
    "galGal", "hg", "mm", "rheMac", "Malaria", "panTro", "rn", 
    "sacCer", "susScr", "xenTro")

# These are the only formats supported by getgo at the
# moment, the purpose is to convert the USCC gene ID formats,
# to the shorthand used by the bioconductor organism
# packages, .e.g. 'refGene'->'ENSEMBL'
.ID_MAP = c("eg", "eg", "ENSEMBL", "SYMBOL", "sgd", "plasmo", 
    "tair")
names(.ID_MAP) = c("knownGene", "refGene", "ensGene", "geneSymbol", 
    "sgd", "plasmo", "tair")

# Below are the exceptions to the function name for gene to
# go term mappings
.ORG_GOMAP_FUNCTION = c("GO2ALLEGS", "GO2ALLTAIRS", "GO2ALLORFS", 
    "GO2ALLORFS")
names(.ORG_GOMAP_FUNCTION) = c("default", "org.At.tair", "org.Pf.plasmo", 
    "org.Sc.sgd")

# TxDb Length databases
.TXDB_ORGS = c("ce6", "dm3", "hg18", "hg19", "hg38", "mm10", 
    "mm9", "rn4", "rn5", "sacCer2", "sacCer3")