R/select_method.R

In IOBR/IOBR: Immune Oncology Biological Research

#' Choose which method to conduct following analysis
#'
#' @param data signature matrix
#' @param method choose method to analysis, contain three methodologies : PCA, ssGSEA, zScore
#'
#' @return filtered signature score matrix
#' @export
#'
#' @examples
#' data(eset_stad, package = "IOBR")
#' eset <- count2tpm(eset_stad, idType = "ensembl")
#' head(eset)
#' eset <- scale_matrix(eset, manipulate = TRUE)
#'
#' res  <- calculate_sig_score(eset = eset, signature = signature_collection[1:4], method = "integration")
#' head(res)
#' res <- select_method(res, method = "PCA")
#' head(res)

select_method<-function(data, method = "ssGSEA" ){


  method<-tolower(method)

  if (method=="ssgsea") {
    data<-data[,-grep(colnames(data),pattern = "_PCA")]
    data<-data[,-grep(colnames(data),pattern = "_zscore")]
    colnames(data)<-gsub(colnames(data),pattern = "_ssGSEA",replacement = "")
  }
  if (method=="pca") {
    data<-data[,-grep(colnames(data),pattern = "_ssGSEA")]
    data<-data[,-grep(colnames(data),pattern = "_zscore")]
    colnames(data)<-gsub(colnames(data),pattern = "_PCA",replacement = "")
  }
  if (method=="zscore") {
    data<-data[,-grep(colnames(data),pattern = "_ssGSEA")]
    data<-data[,-grep(colnames(data),pattern = "_PCA")]
    colnames(data)<-gsub(colnames(data),pattern = "_zscore",replacement = "")
  }
  return(data)
}