R/MMRFquery.R

In MarzyUnicz/MMRFBiolinksX:

#' @title Retrieve sample types.
#' @description
#'   getSampleTypes returns shortLetterCode and definition of type samples in MMRF-COMMPASS Project.
#' @export
#' @examples
#' getSampleTypes()
#'\tabular{ll}{
#'TB \tab   Primary Blood Derived Cancer-Peripheral Blood \cr
#'TRBM \tab Recurrent Blood Derived Cancer-Bone Marrow \cr
#'TBM \tab  Primary Blood Derived Cancer-Bone Marrow \cr
#'NB \tab   Blood Derived Normal \cr
#'TRB \tab Recurrent Blood Derived Cancer - Peripheral Blood \cr
#'}

#' @return a list of barcode filtered by  sample or  tissue type selected



getSampleTypes <- function(){
  sample_type.def <- c("Recurrent Blood Derived Cancer - Bone Marrow",
                       "Primary Blood Derived Cancer - Bone Marrow",
                       "Blood Derived Normal",
                       "Primary Blood Derived Cancer - Peripheral Blood",
                       "Recurrent Blood Derived Cancer - Peripheral Blood")
  sample_type.code <- c("TRBM","TBM","NB","TB","TRB")

  aux <- data.frame(sample_type.code = sample_type.code,sample_type.def)


  return(aux)
}