R/list_platforms.R

In iaradsouza1/MicroarrayMethods: Provide methods for microarray analysis

#' List microarray platforms
#'
#' List microarray platforms annotation available for organisms
#'
#' @param dataset ENSEMBL dataset name. A dataset name can be retrieved with list_datasets() function.
#' @param db One of the following ENSEMBL databases: "main" for ENSEMBL_MART_ENSEMBL database (the main database in ENSEMBL, provides information for the majority of species)
#' and "mouse" for ENSEMBL_MART_MOUSE database (which provides specific information of mouse strains)
#'
#' @return
#' @export
#'
#' @examples
list_platforms <- function(dataset, db = "main")  {
  if (db == "main") {
    ensembl <- biomaRt::useDataset(dataset = dataset, mart = biomaRt::useMart("ENSEMBL_MART_ENSEMBL"))
    att <- biomaRt::listAttributes(ensembl)
    idx <- grep("affy|agilent|illumina", att$description, ignore.case = T)
    att <- att[idx, c(1,2)]
    return(att)
  } else if (db == "mouse") {
    ensembl <- biomaRt::useDataset(dataset = dataset, mart = biomaRt::useMart("ENSEMBL_MART_MOUSE"))
    att <- biomaRt::listAttributes(ensembl)
    idx <- grep("affy|agilent|illumina", att$description, ignore.case = T)
    att <- att[idx, c(1,2)]
    return(att)
  } else {
    stop("Provide an ensembl value: \n 'main': corresponding to ENSEMBL_MART_ENSEMBL database or 'mouse': corresponding to ENSEMBL_MART_MOUSE database")
  }
}