R/Singscore.R

In libcell/deconvBench: A tool for approaches evaluation of cell fraction estimation

#' singscore
#'
#' @param bulkdata A matrix with genes in rows and samples in columns.
#' @param tissue  One of "BLOOD","LIVER","LUNG","MUSCLE","OVARY","HEART","BONE",
#'  "ESOPHAGUS","STOMACH","GASTRIC","PANCREAS","CEREBELLUM",
#'  "NEUROTYPES","RETINA","EYE","THYMUS","INTESTINE","ADRENAL",
#'  "ESOPHAGEAL","DUODENAL","OLFACTORY","CEREBRUM".
#' @importFrom singscore rankGenes simpleScore
#' @importFrom GSEABase getGmt
#' @return  A data frame of Mixed cellular fractions.
#' @export
#' @examples
#'
#'  Bulk <- Bulk_GSE60424
#'  res <- Singscore(bulkdata = Bulk,
#'                   tissue = "BLOOD")
#'
#'



Singscore <- function(bulkdata,tissue) {


  rankData <- singscore::rankGenes(bulkdata)


  probpath <- system.file("extdata", "c8.all.v7.4.symbols.gmt", package = "deconvBench")

  geneset <- GSEABase::getGmt(probpath)

  Tissue <- c("BLOOD","LIVER","LUNG","MUSCLE","OVARY","HEART","BONE",
              "ESOPHAGUS","STOMACH","GASTRIC","PANCREAS","CEREBELLUM",
              "NEUROTYPES","RETINA","EYE","THYMUS","INTESTINE","ADRENAL",
              "ESOPHAGEAL","DUODENAL","OLFACTORY","CEREBRUM")

if(any(Tissue==tissue)){

    tissue_geneset <- geneset[names(geneset)[grep(tissue,names(geneset))]]

    singscore_res <- NULL

    for ( aaa in tissue_geneset) {

      scoredf <- suppressWarnings(singscore::simpleScore(rankData,upSet=aaa))

      singscore_res <- cbind(singscore_res,scoredf$TotalScore)
    }

    rownames(singscore_res) <- colnames(rankData)

    colnames(singscore_res) <- names(tissue_geneset)

                      }else{stop("Please enter one of the sample tissue
                                 types:BLOOD,LIVER,LUNG, MUSCLE,OVARY,HEART,BONE,
                                 ESOPHAGUS,STOMACH,GASTRIC,PANCREAS,CEREBELLUM,
                                 NEUROTYPES,RETINA,EYE,THYMUS,INTESTINE,ADRENAL,
                                 ESOPHAGEAL,DUODENAL,OLFACTORY,CEREBRUM")

                      }

  res_Singscore <- singscore_res

  return(res_Singscore)

}