#' @description get variable genes and evalute the cell cycle effect

#' @param seurat.lists: multi seurat object list

#' @parma method: seurat process method

#' @param: return.only.var.gene, vars.to.regress: parameter for SCTranform

#' @param: nfeatures: the number of variable features

variableFeatureSelection <- function(seurat.lists, method = c("Standard", "SCT"), return.only.var.genes = T, nfeatures = 3000, vars.to.regress = c("nCount_RNA", "percent.mt")){

    for (i in 1:length(seurat.lists)) {

        DefaultAssay(seurat.lists[[i]]) <- "RNA"

        if(method == "SCT"){

            seurat.lists[[i]] <- SCTransform(seurat.lists[[i]], variable.features.n = nfeatures, vars.to.regress = vars.to.regress, verbose = FALSE, return.only.var.genes = return.only.var.genes)

        }else{

            seurat.lists[[i]] <- NormalizeData(seurat.lists[[i]], verbose = FALSE)

            seurat.lists[[i]] <- FindVariableFeatures(seurat.lists[[i]], selection.method = "vst", nfeatures = nfeatures, verbose = FALSE)            

        }

    }

    return(seurat.lists)

}