R对象保存格式RData_RDS_qs2

# =============================================================
# R 单细胞对象保存格式选择：RData / RDS / qs2
# 来源：https://mp.weixin.qq.com/s/cWuCCcCfAaFcdbbmkpn_hQ
# 整理日期：2026-08-22
# 适用对象：Seurat、SingleCellExperiment、大矩阵、列表等
# 使用方式：把下方代码中的 sce.all / group / dat 替换为真实对象
# =============================================================

# 0. 安装 qs2（仅 .qs2 格式需要）
if (!requireNamespace("qs2", quietly = TRUE)) {
  install.packages("qs2")
}

# 1. .RData / .rda：一个文件保存多个带名称对象
# 读取时 load() 会直接把对象放回当前环境，注意同名覆盖
save(sce.all, top5, mycolors, file = "sce_total.RData")
load("sce_total.RData")

# 2. .rds：保存单个对象，读取时返回变量，不会自动污染环境
saveRDS(sce.all, file = "sce.all.rds")
sce.all <- readRDS("sce.all.rds")

# 多个内容先整理成 list，再保存为一个 .rds
result <- list(sce = sce.all, group = group, dat = dat)
saveRDS(result, "analysis_result.rds")
result <- readRDS("analysis_result.rds")
sce.all <- result$sce
group <- result$group
dat <- result$dat

# 3. qs2：新格式，读写通常更快，但需要额外依赖
library(qs2)
qs_save(sce.all, "sce.all.qs2")
sce.all <- qs_read("sce.all.qs2")

# qs2 转回 RDS，方便发送给未安装 qs2 的环境
qs2::qs_to_rds(
  input_file = "sce.all.qs2",
  output_file = "sce.all.rds"
)
sce.all <- readRDS("sce.all.rds")

# 4. 简单基准测试：在真实单细胞对象上比较耗时和文件大小
benchmark_save_formats <- function(obj, tag = "sce", times = 1) {
  library(qs2)
  formats <- c("rdata" = ".RData", "rds" = ".rds", "qs2" = ".qs2")
  result <- lapply(formats, function(ext) {
    path <- paste0(tag, ext)
    time <- system.time({
      for (i in seq_len(times)) {
        if (ext == ".RData") {
          save(obj, file = path)
        } else if (ext == ".rds") {
          saveRDS(obj, file = path)
        } else {
          qs_save(obj, file = path)
        }
      }
    })["elapsed"]
    data.frame(
      format = ext,
      elapsed_sec = unname(time),
      file_size_mb = file.info(path)$size / 1024^2,
      stringsAsFactors = FALSE
    )
  })
  do.call(rbind, result)
}

# 示例：benchmark_save_formats(seurat_obj, tag = "oral_sc", times = 1)