{"id":66551,"date":"2026-11-15T21:15:00","date_gmt":"2026-11-15T13:15:00","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=66551"},"modified":"2026-11-15T14:01:11","modified_gmt":"2026-11-15T06:01:11","slug":"rental-q015-a","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/rental-q015-a\/","title":{"rendered":"\u5206\u6b65\u9aa4\u8bb0\u5f55\u6574\u5408\u8017\u65f6\u5e76\u6838\u5bf9\u7b97\u6cd5\u4e0e\u5bf9\u8c61\u5927\u5c0f"},"content":{"rendered":"

<\/p>\n

\n
\"\u5148\u62c6\u5f00\u6574\u5408\u6d41\u7a0b\u518d\u5b9a\u4f4d\u6162\u70b9\uff1a\u6838\u5bf9sample\u4e0elayer\uff1b\u9010\u9636\u6bb5\u4fdd\u5b58\u65f6\u95f4\u8bb0\u5f55\uff1b\u5355\u72ec\u6d4b\u5fc5\u8981\u9636\u6bb5\u5cf0\u503c\uff1b\u540c\u65f6\u9a8c\u6536\u751f\u7269\u7ed3\u679c\"
\u672c\u6587\u64cd\u4f5c\u4e0e\u68c0\u67e5\u8def\u5f84\u793a\u610f\u3002<\/figcaption><\/figure>\n

\u201c\u6574\u5408\u8dd1\u4e86\u5f88\u4e45\u201d\u53ef\u80fd\u6307\u5f52\u4e00\u5316\u3001\u7f29\u653e\u3001PCA\u3001\u6574\u5408\u672c\u8eab\uff0c\u4e5f\u53ef\u80fd\u662fUMAP\u6216\u4fdd\u5b58\u6587\u4ef6\u3002\u53ea\u5728\u6700\u540e\u770b\u4e00\u6b21\u603b\u8017\u65f6\uff0c\u65e0\u6cd5\u77e5\u9053\u5e94\u8c03\u6574\u54ea\u4e00\u4e2a\u6b65\u9aa4\u3002\u672c\u6587\u5c06Seurat layer\u5de5\u4f5c\u6d41\u62c6\u6210\u53ef\u8bb0\u5f55\u9636\u6bb5\uff0c\u5e2e\u52a9\u628a\u6027\u80fd\u95ee\u9898\u4e0e\u7b97\u6cd5\u9009\u62e9\u5206\u5f00\u3002<\/p>\n

\u793a\u4f8b\u91c7\u7528\u652f\u6301Assay5\u7684Seurat\u7248\u672c\uff0c\u8f93\u5165\u662f\u5df2\u5b8c\u6210\u8d28\u91cf\u6838\u67e5\u3001\u53ea\u6709\u4e00\u4e2aRNA counts\u5c42\u7684\u5185\u5b58\u578b\u5bf9\u8c61\uff0c\u5e76\u6709\u53ef\u9760\u7684sample_id\u5217\u3002\u4ee3\u7801\u4f7f\u7528\u5f53\u524d\u516c\u5f00\u7684IntegrateLayers\u63a5\u53e3\uff1b\u65e7anchor\u5bf9\u8c61\u6d41\u7a0b\u4e0e\u65b0\u7684layer\u6d41\u7a0b\u4e0d\u8981\u6df7\u5728\u540c\u4e00\u4efd\u811a\u672c\u91cc\u3002\u78c1\u76d8\u77e9\u9635\u7684\u4fdd\u5b58\u548c\u7269\u5316\u95ee\u9898\u9700\u8981\u53e6\u884c\u68c0\u67e5\uff0c\u4e0d\u80fd\u76f4\u63a5\u7167\u642c\u5185\u5b58\u5bf9\u8c61\u7684\u4f30\u7b97\u3002<\/p>\n

\u5148\u786e\u8ba4\u6574\u5408\u76ee\u6807\u548c\u8f93\u5165\u5206\u5c42<\/h2>\n

\u5199\u6e05\u54ea\u4e9b\u53d8\u91cf\u4ee3\u8868\u6280\u672f\u6279\u6b21\uff0c\u54ea\u4e9b\u4ee3\u8868\u771f\u5b9e\u751f\u7269\u5dee\u5f02\u3002\u5c06\u5904\u7406\u6761\u4ef6\u3001\u75be\u75c5\u72b6\u6001\u6216\u7ec4\u7ec7\u6765\u6e90\u76f4\u63a5\u5f53\u4f5c\u9700\u8981\u5b8c\u5168\u6d88\u9664\u7684\u6279\u6b21\uff0c\u53ef\u80fd\u635f\u5931\u7814\u7a76\u4fe1\u53f7\u3002\u6027\u80fd\u4f18\u5316\u4e4b\u524d\uff0c\u9700\u8981\u65b9\u6cd5\u672c\u8eab\u9002\u7528\u4e8e\u6570\u636e\uff1b\u6700\u5feb\u5b8c\u6210\u7684\u4e00\u6b21\u8fd0\u884c\u4e0d\u4e00\u5b9a\u662f\u5408\u9002\u7684\u6574\u5408\u3002<\/p>\n

\u68c0\u67e5\u6bcf\u4e2a\u6837\u672c\u7ec6\u80de\u6570\u3001\u5171\u540c\u7279\u5f81\u3001assay\u4e0elayer\u72b6\u6001\u3002\u4e00\u4e2a\u5df2\u7ecf\u6309\u6837\u672c\u62c6\u5f00\u7684assay\uff0c\u4e0d\u5e94\u518d\u6b21\u65e0\u6761\u4ef6split\u3002\u82e5\u5bf9\u8c61\u8fd8\u4fdd\u5b58\u591a\u4efd\u4e0d\u518d\u9700\u8981\u7684\u6574\u5408\u7ed3\u679c\uff0c\u5148\u786e\u8ba4\u4fdd\u7559\u7528\u9014\u5e76\u5f52\u6863\uff1b\u4e0d\u8981\u5728\u540c\u4e00\u4e2a\u6d3b\u52a8\u5bf9\u8c61\u4e2d\u4e0d\u65ad\u53e0\u52a0\u5019\u9009\u65b9\u6cd5\u540e\uff0c\u518d\u628a\u5bf9\u8c61\u81a8\u80c0\u90fd\u5f52\u7ed3\u4e3a\u7b97\u6cd5\u6162\u3002<\/p>\n

\u7ed9\u6bcf\u4e2a\u9636\u6bb5\u5efa\u7acb\u65f6\u95f4\u8bb0\u5f55<\/h2>\n

\u4e0b\u9762\u7684\u8ba1\u65f6\u5305\u88c5\u5668\u8bb0\u5f55\u5899\u949f\u65f6\u95f4\u548c\u8fd4\u56de\u5bf9\u8c61\u7684\u8fd1\u4f3c\u5927\u5c0f\u3002\u5bf9\u8c61\u5927\u5c0f\u4e0d\u80fd\u66ff\u4ee3R\u8fdb\u7a0b\u7684\u5cf0\u503c\u5185\u5b58\uff0c\u56e0\u6b64\u8fd0\u884c\u6574\u4efd\u811a\u672c\u65f6\u8fd8\u8981\u914d\u5408\u5916\u90e8\u7edf\u8ba1\u3002\u793a\u4f8b\u4e2d\u7684\u7ef4\u5ea6\u4e0a\u9650\u662f\u6f14\u793a\u8d77\u70b9\uff0c\u5b9e\u9645\u5206\u6790\u8981\u7ed3\u5408\u6570\u636e\u4e0e\u76ee\u6807\u9009\u62e9\u3002<\/p>\n

library(Seurat)\nobj <- readRDS("qc-counts-only.rds")\nDefaultAssay(obj) <- "RNA"\nstopifnot(inherits(obj[["RNA"]], "Assay5"),\n          identical(Layers(obj[["RNA"]]), "counts"),\n          "sample_id" %in% colnames(obj[[]]), !anyNA(obj$sample_id),\n          all(nzchar(obj$sample_id)), length(unique(obj$sample_id))>=2L)\nwrite.csv(data.frame(step=character(), elapsed=numeric(), bytes=numeric()),\n          "stage-times.csv", row.names=FALSE)\nmeasure <- function(label, expr) {\n  timing <- system.time(ans <- force(expr))\n  row <- data.frame(step=label, elapsed=unname(timing["elapsed"]),\n                    bytes=as.numeric(object.size(ans)))\n  write.table(row, "stage-times.csv", sep=",", append=TRUE,\n              col.names=FALSE, row.names=FALSE)\n  ans\n}\nobj[["RNA"]] <- split(obj[["RNA"]], f=obj$sample_id)\nobj <- measure("normalize", NormalizeData(obj))\nobj <- measure("features", FindVariableFeatures(obj))\nobj <- measure("scale", ScaleData(obj, features=VariableFeatures(obj)))\nnpcs <- min(30L, length(VariableFeatures(obj))-1L,\n            min(table(obj$sample_id))-1L)\nstopifnot(npcs >= 2L)\nobj <- measure("pca", RunPCA(obj, npcs=npcs))\nsaveRDS(obj, "prepared-before-integration.rds")\nobj <- measure("rpca", IntegrateLayers(obj, method=RPCAIntegration,\n              orig.reduction="pca", new.reduction="integrated.rpca",\n              dims=seq_len(npcs), verbose=TRUE))\nsaveRDS(obj, "integrated-rpca.rds")<\/code><\/pre>\n\n\n\n\n\n\n\n\n\n
\u65f6\u95f4\u4e3b\u8981\u82b1\u5728\u54ea\u91cc<\/th>\n\u7ee7\u7eed\u6838\u5bf9\u7684\u5185\u5bb9<\/th>\n\u53ef\u80fd\u7684\u5408\u7406\u8c03\u6574<\/th>\n<\/tr>\n<\/thead>\n
\u5f52\u4e00\u5316\u6216\u7279\u5f81\u51c6\u5907<\/td>\n\u662f\u5426\u91cd\u590d\u5904\u7406\uff0c\u5c42\u7ed3\u6784\u662f\u5426\u6b63\u786e<\/td>\n\u590d\u7528\u5df2\u9a8c\u6536\u51c6\u5907\u8282\u70b9<\/td>\n<\/tr>\n
ScaleData<\/td>\n\u5b9e\u9645\u7279\u5f81\u8303\u56f4\u3001\u56de\u5f52\u9879\u548c\u77e9\u9635\u8868\u793a<\/td>\n\u5728\u65b9\u6cd5\u5141\u8bb8\u65f6\u7f29\u5c0f\u4e0d\u5fc5\u8981\u8303\u56f4<\/td>\n<\/tr>\n
PCA<\/td>\n\u7ec6\u80de\u91cf\u3001\u7279\u5f81\u91cf\u3001\u7ef4\u5ea6\u4e0e\u540e\u7aef<\/td>\n\u6bd4\u8f83\u9002\u7528\u7ef4\u5ea6\u548c\u5b9e\u73b0\u6761\u4ef6<\/td>\n<\/tr>\n
IntegrateLayers<\/td>\n\u65b9\u6cd5\u3001\u6837\u672c\u89c4\u6a21\u3001\u53c2\u8003\u9009\u62e9\u4e0e\u53c2\u6570<\/td>\n\u6309\u751f\u7269\u76ee\u6807\u6bd4\u8f83\u5019\u9009\u7b56\u7565<\/td>\n<\/tr>\n
UMAP\u6216\u4fdd\u5b58<\/td>\n\u662f\u5426\u8bef\u7b97\u6210\u6574\u5408\u672c\u8eab\uff0c\u5b58\u50a8\u662f\u5426\u53d7\u9650<\/td>\n\u5206\u522b\u8bb0\u5f55\u5e76\u5904\u7406\u56fe\u5f62\u6216I\/O\u9700\u6c42<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n
\u600e\u6837\u8bfb\u53d6\u8ba1\u65f6\u4e0e\u5185\u5b58\u8bc1\u636e<\/h2>\n
\u4f7f\u7528\/usr\/bin\/time -v Rscript your-script.R<\/code>\u8bb0\u5f55\u6574\u6bb5\u4efb\u52a1\uff1b\u82e5\u6700\u9ad8\u5185\u5b58\u9636\u6bb5\u4ecd\u4e0d\u6e05\u695a\uff0c\u53ef\u4ece\u5df2\u7ecf\u4fdd\u5b58\u7684\u51c6\u5907\u8282\u70b9\u542f\u52a8\u5355\u4e00\u9636\u6bb5\u8fdb\u884c\u6d4b\u91cf\u3002\u9636\u6bb5\u5bf9\u8c61\u5927\u5c0f\u8f83\u5c0f\uff0c\u4e0d\u4fdd\u8bc1\u6784\u5efa\u5b83\u7684\u8fc7\u7a0b\u4e2d\u6ca1\u6709\u51fa\u73b0\u66f4\u5927\u7684\u4e34\u65f6\u77e9\u9635\u6216\u5e76\u884c\u526f\u672c\u3002<\/p>\n
\u5982\u679cCPU\u672a\u6ee1\uff0c\u5148\u67e5\u770b\u5b9e\u9645\u7b97\u6cd5\u3001\u7b49\u5f85I\/O\u4e0e\u4e2a\u4eba\u8d44\u6e90\u989d\u5ea6\uff0c\u800c\u4e0d\u662f\u76f4\u63a5\u8ffd\u52a0\u6838\u5fc3\u3002\u82e5\u51fa\u73b0future\u53d8\u91cf\u5bfc\u51fa\u4e0a\u9650\uff0c\u6309\u5b8c\u6574\u9519\u8bef\u533a\u5206\u5bfc\u51fa\u8bbe\u7f6e\u548c\u7269\u7406\u5185\u5b58\u95ee\u9898\u3002\u82e5\u62a5\u9519\u4e0e\u7279\u5f81\u7f3a\u5931\u3001\u6837\u672c\u592a\u5c0f\u6216\u5c42\u7ed3\u6784\u6709\u5173\uff0c\u5148\u4fee\u590d\u8f93\u5165\u548c\u65b9\u6cd5\u6761\u4ef6\uff0c\u786c\u4ef6\u6269\u5bb9\u4e0d\u80fd\u66ff\u4ee3\u8fd9\u4e9b\u68c0\u67e5\u3002<\/p>\n
\u9a8c\u6536\u6574\u5408\u7ed3\u679c\u548c\u4e0b\u4e00\u6b65<\/h2>\n
\u786e\u8ba4\u76ee\u6807reduction\u5b58\u5728\uff0c\u7ec6\u80de\u540d\u548c\u5143\u6570\u636e\u5bf9\u5e94\uff0c\u4fdd\u5b58\u6587\u4ef6\u53ef\u4ee5\u91cd\u65b0\u8bfb\u53d6\u3002\u8fdb\u4e00\u6b65\u7528\u6279\u6b21\u3001\u6837\u672c\u548c\u53ef\u4fe1\u7ec6\u80de\u7c7b\u578b\u5206\u522b\u89c2\u5bdf\u7ed3\u679c\uff0c\u68c0\u67e5\u5df2\u77e5\u7fa4\u4f53\u662f\u5426\u4fdd\u7559\u3002\u4e0d\u80fd\u4ee5\u6240\u6709\u6837\u672c\u5728\u56fe\u4e0a\u6df7\u5f97\u8d8a\u5747\u5300\u8d8a\u597d\u4f5c\u4e3a\u552f\u4e00\u6807\u51c6\uff0c\u4e5f\u4e0d\u80fd\u7528\u6574\u5408\u4f4e\u7ef4\u8868\u793a\u76f4\u63a5\u4ee3\u66ff\u6240\u6709\u5dee\u5f02\u5206\u6790\u6240\u9700\u7684\u8868\u8fbe\u6570\u636e\u3002<\/p>\n
\u603b\u7ec6\u80de\u6570\u4e4b\u5916\u8fd8\u8981\u8bb0\u5f55\u6279\u6b21\u6570<\/h2>\n
\u4e24\u4e2a\u9879\u76ee\u603b\u7ec6\u80de\u6570\u76f8\u8fd1\uff0c\u5e76\u4e0d\u610f\u5473\u7740\u6574\u5408\u4efb\u52a1\u76f8\u540c\u3002\u6837\u672c\u6570\u91cf\u3001\u6837\u672c\u4e4b\u95f4\u53ef\u5bf9\u5e94\u7684\u7ec6\u80de\u7ed3\u6784\u3001\u9009\u7528\u7ef4\u5ea6\u548c\u53c2\u8003\u7b56\u7565\uff0c\u90fd\u53ef\u80fd\u5f71\u54cd\u5de5\u4f5c\u91cf\u4e0e\u7ed3\u679c\u3002\u9636\u6bb5\u8bb0\u5f55\u91cc\u5e94\u5305\u542b\u8fd9\u4e9b\u6761\u4ef6\uff0c\u800c\u4e0d\u662f\u53ea\u586b\u4e00\u4e2a\u7ec6\u80de\u603b\u6570\u3002<\/p>\n
\u82e5\u60f3\u589e\u52a0\u5e76\u884c\u5ea6\uff0c\u5e94\u5148\u6838\u5bf9\u8be5\u65b9\u6cd5\u548c\u7248\u672c\u5b9e\u9645\u4f7f\u7528\u7684\u5e76\u884c\u8def\u5f84\uff0c\u518d\u7528\u540c\u8f93\u5165\u6bd4\u8f83\u3002\u66f4\u591aworker\u53ef\u80fd\u589e\u52a0\u5bf9\u8c61\u526f\u672c\uff0c\u67d0\u4e9b\u9636\u6bb5\u4e5f\u672a\u5fc5\u4ece\u66f4\u591a\u6838\u5fc3\u53d7\u76ca\u3002\u5148\u4fdd\u7559\u4e00\u4e2a\u53ef\u89e3\u91ca\u7684\u57fa\u7ebf\uff0c\u518d\u9010\u9879\u4fee\u6539\u5e76\u53d1\uff0c\u6bd4\u540c\u65f6\u8c03\u5927\u6838\u5fc3\u3001\u5185\u5b58\u548c\u65b9\u6cd5\u53c2\u6570\u66f4\u5bb9\u6613\u5b9a\u4f4d\u95ee\u9898\u3002<\/p>\n
\u6709\u4e86\u9636\u6bb5\u65f6\u95f4\u8868\uff0c\u518d\u9488\u5bf9\u5b9e\u9645\u5fc5\u8981\u9636\u6bb5\u8bc4\u4f30CPU\u3001\u5185\u5b58\u548c\u5de5\u4f5c\u76d8\u3002\u6d41\u7a0b\u4e0e\u65b9\u6cd5\u6761\u4ef6\u5408\u7406\u3001\u5fc5\u8981\u8d44\u6e90\u4ecd\u8d85\u51fa\u672c\u5730\u5bb9\u91cf\u65f6\uff0c\u53ef\u4ee5\u51c6\u5907\u6574\u5408\u65b9\u6cd5\u3001\u6837\u672c\u4e0e\u7ec6\u80de\u89c4\u6a21\u3001\u9636\u6bb5\u65e5\u5fd7\u548c\u4f7f\u7528\u671f\u9650\uff0c\u6c9f\u901a\u5927\u5185\u5b58CPU\u670d\u52a1\u5668\u65b9\u6848\u3002<\/p>\n
\u53c2\u8003\u4e0e\u7248\u672c\u6838\u5bf9<\/h2>\n