{"id":68240,"date":"2026-11-14T20:28:55","date_gmt":"2026-11-14T12:28:55","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=68240"},"modified":"2026-11-14T20:28:55","modified_gmt":"2026-11-14T12:28:55","slug":"archr-pseudobulk-reproducible-peaks-donor-support","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/archr-pseudobulk-reproducible-peaks-donor-support\/","title":{"rendered":"ArchR \u7684\u5cf0\u80fd\u5728\u4e24\u4efd\u4f2a\u6c47\u603b\u91cc\u91cd\u590d\uff0c\u5c31\u80fd\u8bf4\u6709\u4e24\u540d\u4f9b\u4f53\u652f\u6301\u5417\uff1f"},"content":{"rendered":"
\n

\u5355\u7ec6\u80de\u5f00\u653e\u67d3\u8272\u8d28\u6570\u636e\u5f88\u7a00\u758f\uff0c\u628a\u540c\u4e00\u7c7b\u578b\u7684\u7ec6\u80de\u6c47\u603b\u8d77\u6765\uff0c\u539f\u6765\u51e0\u4e4e\u770b\u4e0d\u89c1\u7684\u5c40\u90e8\u63d2\u5165\u4fe1\u53f7\u4f1a\u53d8\u5f97\u6e05\u695a\u3002ArchR \u5229\u7528\u8fd9\u79cd\u601d\u8def\u5efa\u7acb\u5206\u7ec4\u8986\u76d6\u6587\u4ef6\uff0c\u518d\u8bc6\u522b\u4e00\u7ec4\u53ef\u91cd\u590d\u7684\u5cf0\u3002\u4e00\u4efd\u770b\u4f3c\u4e25\u8c28\u7684\u7ed3\u679c\u5199\u7740\u201c\u8be5\u4f4d\u70b9\u5728\u4e24\u4e2a\u91cd\u590d\u4e2d\u51fa\u73b0\u201d\uff0c\u4f46\u5b9e\u9a8c\u8bb0\u5f55\u91cc\u6b64\u7c7b\u7a00\u6709\u7ec6\u80de\u53ea\u6765\u81ea\u4e00\u540d\u4f9b\u4f53\u3002\u8fd9\u4e0d\u4e00\u5b9a\u662f\u8f6f\u4ef6\u51fa\u4e86\u9519\u3002\u95ee\u9898\u5728\u4e8e\uff0c\u6b64\u5904\u91cd\u590d\u7684\u662f\u54ea\u4efd\u6750\u6599\u3001\u54ea\u4e00\u6b21\u5212\u5206\uff0c\u4ee5\u53ca\u5b83\u7a76\u7adf\u80fd\u652f\u6301\u54ea\u79cd\u7ed3\u8bba\u3002<\/p>\n

\u628a\u7ec4\u6210\u4f2a\u6c47\u603b\u7684\u6bcf\u4e2a\u7ec6\u80de\u8ffd\u5230\u6837\u672c<\/h2>\n

\u5efa\u5cf0\u524d\u5148\u505a\u4e00\u4e2a\u7ec6\u80de\u7c7b\u578b\u4e58\u4f9b\u4f53\u7684\u8868\uff0c\u9664\u4e86\u7ec6\u80de\u6570\u518d\u5217\u5404\u683c\u7684\u6709\u6548\u7247\u6bb5\u6570\u3002\u4e24\u540d\u4f9b\u4f53\u540c\u6837\u8d21\u732e\u56db\u5341\u679a\u7ec6\u80de\uff0c\u82e5\u5176\u4e2d\u4e00\u4efd\u7247\u6bb5\u6df1\u5ea6\u53ea\u6709\u53e6\u4e00\u4efd\u7684\u51e0\u5206\u4e4b\u4e00\uff0c\u53d1\u73b0\u8f83\u5f31\u5f00\u653e\u4f4d\u70b9\u7684\u80fd\u529b\u53ef\u80fd\u76f8\u5dee\u5f88\u5927\u3002\u5bf9\u4e8e\u7a00\u6709\u7fa4\uff0c\u8fd8\u8981\u770b\u8fd9\u4e9b\u7ec6\u80de\u662f\u5426\u5206\u5e03\u5728\u591a\u4e2a\u6837\u672c\uff0c\u6216\u662f\u5426\u5168\u90e8\u6765\u81ea\u4e00\u6b21\u89e3\u79bb\u3002\u5148\u786e\u5b9a\u60f3\u5efa\u7acb\u54ea\u4e2a\u5c42\u7ea7\u7684\u5cf0\u96c6\uff0c\u518d\u9009\u62e9\u6309\u7c97\u8c31\u7cfb\u3001\u7ec6\u5206\u7c7b\u522b\u8fd8\u662f\u5b9e\u9a8c\u5904\u7406\u6765\u5206\u7ec4\u3002<\/p>\n

ArchR \u7684\u5206\u7ec4\u8986\u76d6\u51fd\u6570\u53ef\u4ee5\u5229\u7528\u6837\u672c\u6807\u7b7e\u5212\u5206\u4f2a\u6c47\u603b\u3002\u4f20\u5165\u7684\u5206\u7ec4\u5b57\u6bb5\u51b3\u5b9a\u54ea\u4e9b\u7ec6\u80de\u88ab\u653e\u5728\u540c\u4e00\u7c7b\u4e2d\uff0c\u6837\u672c\u6807\u7b7e\u5219\u6709\u52a9\u4e8e\u5728\u7c7b\u5185\u5229\u7528\u6765\u6e90\u4fe1\u606f\u3002\u7ec6\u80de\u5f88\u5c11\u65f6\uff0c\u9879\u76ee\u5185\u5bb9\u548c\u53c2\u6570\u4f1a\u7ea6\u675f\u80fd\u5efa\u7acb\u54ea\u4e9b\u91cd\u590d\uff0c\u4e0d\u80fd\u4ec5\u9760\u8f93\u51fa\u6587\u4ef6\u540d\u63a8\u65ad\u8fd9\u4e9b\u91cd\u590d\u6765\u81ea\u54ea\u4e9b\u4f9b\u4f53\u3002\u5efa\u8bae\u5f52\u6863\u6bcf\u4e2a\u91cd\u590d\u91cc\u7684\u7ec6\u80de\u3001\u6587\u5e93\u548c\u5b9e\u9645\u7247\u6bb5\u6570\uff0c\u5c24\u5176\u8981\u67e5\u4e24\u4e2a\u6587\u4ef6\u662f\u5426\u5171\u4eab\u6765\u6e90\u6216\u90e8\u5206\u6761\u5f62\u7801\u3002\u4e00\u4e2a\u5927\u7fa4\u6bcf\u4e2a\u91cd\u590d\u90fd\u5f88\u6df1\u7684\u65f6\u5019\uff0c\u4ece\u4e2d\u5b66\u5f97\u7684\u76f4\u89c9\u672a\u5fc5\u9002\u7528\u4e8e\u4e00\u4e2a\u7a00\u6709\u7fa4\u3002ArchR \u7684\u4f2a\u6c47\u603b\u6784\u5efa\u6559\u7a0b<\/a><\/p>\n

\u7528\u4e24\u4e2a\u4f4d\u70b9\u533a\u5206\u6df1\u5ea6\u91cd\u590d\u548c\u751f\u7269\u5b66\u91cd\u590d<\/h2>\n

\u5047\u8bbe\u6559\u5b66\u6570\u636e\u91cc\uff0c\u7532\u4f9b\u4f53\u7684\u540c\u7c7b\u7ec6\u80de\u5f88\u591a\uff0c\u62c6\u6210\u7532\u4e00\u548c\u7532\u4e8c\uff0c\u4e59\u4f9b\u4f53\u5355\u72ec\u5f62\u6210\u4e00\u4efd\u8986\u76d6\u6587\u4ef6\u3002\u4f4d\u70b9\u7532\u5728\u7532\u4e00\u3001\u7532\u4e8c\u4e2d\u90fd\u5f62\u6210\u5cf0\uff0c\u4e59\u6ca1\u6709\u5f62\u6210\u5cf0\u3002\u4f4d\u70b9\u4e59\u5728\u7532\u4e00\u548c\u4e59\u4e2d\u5f62\u6210\u5cf0\uff0c\u7532\u4e8c\u6ca1\u6709\u3002\u82e5\u53ea\u6570\u4e09\u4e2a\u6587\u4ef6\u4e2d\u6709\u51e0\u4e2a\u6253\u52fe\uff0c\u4e24\u4e2a\u4f4d\u70b9\u90fd\u5f97\u5230\u4e8c\u3002\u82e5\u6539\u6570\u6709\u51e0\u4e2a\u4e0d\u540c\u4f9b\u4f53\u63d0\u4f9b\u8fc7\u652f\u6301\uff0c\u4f4d\u70b9\u7532\u53ea\u6709\u4e00\u4e2a\uff0c\u4f4d\u70b9\u4e59\u6709\u4e24\u4e2a\u3002\u4e24\u79cd\u90fd\u503c\u5f97\u7559\u4e0b\uff0c\u4f46\u5e94\u5e26\u7740\u4e0d\u540c\u7684\u8bc1\u636e\u8bf4\u660e\u8fdb\u5165\u540e\u7eed\u5206\u6790\u3002<\/p>\n

\n\n\n\n\n\n\n
\u6559\u5b66\u4f4d\u70b9<\/th>\n\u7532\u4e00<\/th>\n\u7532\u4e8c<\/th>\n\u4e59<\/th>\n\u6709\u4fe1\u53f7\u7684\u72ec\u7acb\u4f9b\u4f53<\/th>\n<\/tr>\n<\/thead>\n
\u4f4d\u70b9\u7532<\/td>\n\u6709\u5cf0<\/td>\n\u6709\u5cf0<\/td>\n\u672a\u6210\u5cf0<\/td>\n1<\/td>\n<\/tr>\n
\u4f4d\u70b9\u4e59<\/td>\n\u6709\u5cf0<\/td>\n\u672a\u6210\u5cf0<\/td>\n\u6709\u5cf0<\/td>\n2<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"\u4e24\u4e2a\u6587\u4ef6\u6709\u5cf0\uff0c\u6765\u81ea\u51e0\u540d\u4f9b\u4f53\u3002\u6559\u5b66\u7b97\u4f8b\uff5c\u7532\u4f9b\u4f53\u62c6\u6210\u4e24\u4efd\uff0c\u4e59\u4f9b\u4f53\u4fdd\u7559\u4e00\u4efd\u3002\u4f4d\u70b9\u7532\uff0c\u7532\u4e00\u3001\u7532\u4e8c\u5206\u522b\u6210\u5cf0\uff0c\u4e24\u4efd\u8986\u76d6\u7ed9\u51fa\u652f\u6301\uff0c\u6765\u81ea\u540c\u4e00\u540d\u4f9b\u4f53\u3002\u4f4d\u70b9\u4e59\uff0c\u7532\u4e00\u3001\u4e59\u5206\u522b\u6210\u5cf0\uff0c\u540c\u6837\u662f\u4e24\u4efd\u8986\u76d6\uff0c\u8fd9\u6b21\u6709\u4e24\u540d\u4f9b\u4f53\u3002\u67e5\u539f\u56fe\uff0c\u67e5\u8986\u76d6\u6df1\u5ea6\u3001\u5750\u6807\u548c\u8fb9\u754c\uff0c\u672a\u8fbe\u5230\u5cf0\u8c03\u7528\u9608\u503c\u7684\u6837\u672c\u8fd8\u53ef\u80fd\u6709\u5c40\u90e8\u63d2\u5165\u3002\"
\u6559\u5b66\u7b97\u4f8b\uff5c\u7532\u4f9b\u4f53\u62c6\u6210\u4e24\u4efd\uff0c\u4e59\u4f9b\u4f53\u4fdd\u7559\u4e00\u4efd\u3002<\/figcaption><\/figure>\n

\u8868\u91cc\u7684\u201c\u672a\u6210\u5cf0\u201d\u4e5f\u4e0d\u8981\u5199\u6210\u201c\u5b8c\u5168\u5173\u95ed\u201d\u3002\u5cf0\u8c03\u7528\u8981\u7efc\u5408\u5c40\u90e8\u63d2\u5165\u548c\u80cc\u666f\uff0c\u8f83\u6d45\u7684\u91cd\u590d\u53ef\u80fd\u53ea\u6709\u5c11\u91cf\u8bfb\u6bb5\uff0c\u5c1a\u4e0d\u8db3\u4ee5\u8fbe\u5230\u5224\u5cf0\u6807\u51c6\u3002\u9488\u5bf9\u6bcf\u4e00\u5904\u5019\u9009\uff0c\u628a\u76f8\u540c\u57fa\u56e0\u7ec4\u5750\u6807\u4e0a\u7684\u539f\u59cb\u5206\u7ec4\u8986\u76d6\u753b\u5728\u540c\u4e00\u7eb5\u8f74\u6216\u91c7\u7528\u4e00\u81f4\u7684\u5f52\u4e00\u5316\u65b9\u5f0f\uff0c\u5e76\u7ed9\u51fa\u5404\u7ec4\u603b\u7247\u6bb5\u6570\u3002\u82e5\u56fe\u81ea\u52a8\u4e3a\u6bcf\u4e00\u884c\u5355\u72ec\u8c03\u6574\u7eb5\u8f74\uff0c\u8f83\u5c0f\u7684\u6ce2\u52a8\u548c\u5f88\u5f3a\u7684\u5bcc\u96c6\u90fd\u80fd\u586b\u6ee1\u6574\u884c\uff0c\u770b\u8d77\u6765\u5f88\u63a5\u8fd1\uff0c\u8bfb\u8005\u5374\u65e0\u6cd5\u76f4\u63a5\u6bd4\u8f83\u91cf\u7ea7\u3002<\/p>\n

\u4ece\u5206\u7ec4\u8986\u76d6\u751f\u6210\u5cf0\u96c6\uff0c\u518d\u56de\u5230\u6bcf\u4e2a\u7ec6\u80de\u8ba1\u6570<\/h2>\n

\u4e0b\u9762\u5047\u8bbe\u5bf9\u8c61\u5df2\u6709\u7ecf\u8fc7\u68c0\u67e5\u7684\u7ec6\u80de\u7c7b\u578b\u5217\u548c\u4f9b\u4f53\u5217\uff0c\u5e76\u5df2\u5b89\u88c5\u53ef\u7528\u7684 MACS2\u3002\u5148\u6309\u7ec6\u80de\u7c7b\u578b\u751f\u6210\u8003\u8651\u4f9b\u4f53\u6807\u7b7e\u7684\u8986\u76d6\uff0c\u518d\u6307\u5b9a\u7528\u540c\u4e00\u5206\u7ec4\u540d\u79f0\u751f\u6210\u53ef\u91cd\u590d\u5cf0\u96c6\u3002\u793a\u4f8b\u4e2d\u7684\u91cd\u590d\u6570\u7528\u6765\u8bf4\u660e\u53c2\u6570\u542b\u4e49\uff0c\u771f\u5b9e\u9879\u76ee\u5e94\u68c0\u67e5\u53c2\u4e0e\u5efa\u5cf0\u7684\u8986\u76d6\u6587\u4ef6\uff0c\u518d\u5224\u65ad\u8fd9\u6837\u7684\u8981\u6c42\u662f\u5426\u9002\u7528\u4e8e\u6bcf\u4e2a\u7ec4\u3002\u6700\u540e\u6784\u5efa\u9010\u7ec6\u80de\u5cf0\u77e9\u9635\uff0c\u4f9b\u540e\u7eed\u5b9a\u91cf\u548c\u53ef\u89c6\u5316\u4f7f\u7528\u3002\u5cf0\u8c03\u7528\u7684\u987a\u5e8f<\/a> \u00b7 \u91cd\u590d\u652f\u6301\u548c\u5cf0\u6570\u9650\u5236\u7684\u53c2\u6570<\/a><\/p>\n

library(ArchR)\r\nmacs <- unname(Sys.which("macs2"))\r\nstopifnot(nzchar(macs))\r\nproj <- addGroupCoverages(ArchRProj = proj, groupBy = "CellType",\r\n                          useLabels = TRUE, sampleLabels = "Donor")\r\nproj <- addReproduciblePeakSet(ArchRProj = proj, groupBy = "CellType",\r\n                               pathToMacs2 = macs, reproducibility = "2")\r\nproj <- addPeakMatrix(proj)\r\n<\/code><\/pre>\n
\u5728\u8f93\u51fa\u4e2d\u627e\u4e0d\u5230\u67d0\u4e00\u7c7b\u7ec6\u80de\u719f\u6089\u7684\u8c03\u63a7\u533a\uff0c\u53ef\u4ee5\u6309\u6b65\u9aa4\u9006\u67e5\u3002\u5148\u786e\u8ba4\u8be5\u7c7b\u662f\u5426\u5f62\u6210\u4e86\u8db3\u591f\u7684\u6709\u6548\u8986\u76d6\uff0c\u518d\u6838\u5bf9\u8fd9\u4e2a\u4f4d\u70b9\u5728\u5404\u4e2a\u72ec\u7acb\u91cd\u590d\u91cc\u6709\u6ca1\u6709\u88ab\u8c03\u7528\u3002\u82e5\u6709\u539f\u59cb\u5cf0\u800c\u6700\u7ec8\u5408\u5e76\u96c6\u5408\u627e\u4e0d\u5230\u539f\u540d\u5b57\uff0c\u67e5\u770b\u662f\u5426\u4e0e\u90bb\u8fd1\u5cf0\u91cd\u53e0\u3001\u88ab\u7edf\u4e00\u4e3a\u65b0\u7684\u8fb9\u754c\u6216\u5728\u9650\u5236\u4fdd\u7559\u5cf0\u6570\u65f6\u843d\u9009\u3002\u4f7f\u7528\u51c6\u786e\u7684\u53c2\u8003\u57fa\u56e0\u7ec4\u548c\u5750\u6807\u68c0\u7d22\uff0c\u6bd4\u62ff\u4e24\u4e2a\u7ed3\u679c\u7684\u884c\u540d\u76f4\u63a5\u6c42\u5b57\u9762\u4ea4\u96c6\u66f4\u53ef\u9760\u3002\u82e5\u533a\u57df\u9760\u8fd1\u88ab\u6392\u9664\u7684\u67d3\u8272\u4f53\u6216\u4f4e\u53ef\u6bd4\u5bf9\u533a\u57df\uff0c\u4e5f\u8981\u68c0\u67e5\u76f8\u5e94\u8bbe\u7f6e\u3002<\/p>\n
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