{"id":67123,"date":"2026-11-14T19:48:22","date_gmt":"2026-11-14T11:48:22","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=67123"},"modified":"2026-11-15T00:06:57","modified_gmt":"2026-11-14T16:06:57","slug":"archr-arrow-fragments-tss-qc-counts","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/archr-arrow-fragments-tss-qc-counts\/","title":{"rendered":"ArchR \u8d28\u63a7\u540e\u7ec6\u80de\u5c11\u4e86\uff0c\u600e\u6837\u67e5\u6e05\u662f\u7247\u6bb5\u6570\u8fd8\u662f TSS \u5bcc\u96c6\u5728\u8d77\u4f5c\u7528\uff1f"},"content":{"rendered":"
\n

\u505a\u5b8c\u5355\u7ec6\u80de ATAC \u8d28\u63a7\uff0c\u6700\u5bb9\u6613\u770b\u5230\u7684\u662f\u201c\u5269\u4e0b\u591a\u5c11\u7ec6\u80de\u201d\uff0c\u6700\u5bb9\u6613\u6f0f\u6389\u7684\u662f\u8fd9\u4e2a\u6570\u5b57\u7684\u5206\u6bcd\u3002\u539f\u59cb\u7247\u6bb5\u6587\u4ef6\u91cc\u51fa\u73b0\u8fc7\u7684\u6761\u7801\u3001\u5199\u5165 Arrow \u7684\u7ec6\u80de\u3001\u8fdb\u5165\u6700\u540e\u5206\u6790\u7684\u7ec6\u80de\uff0c\u662f\u4e09\u4e2a\u4e0d\u540c\u7684\u96c6\u5408\u3002\u628a\u5b83\u4eec\u6df7\u5728\u4e00\u8d77\uff0c\u53ef\u80fd\u4f1a\u8bef\u4ee5\u4e3a\u8c03\u4f4e TSS \u9608\u503c\u5c31\u80fd\u627e\u56de\u5168\u90e8\u7ec6\u80de\u3002\u8981\u627e\u5230\u771f\u6b63\u5f71\u54cd\u6837\u672c\u7684\u90a3\u4e00\u6b65\uff0c\u53ef\u4ee5\u5148\u628a\u6761\u7801\u540d\u5355\u9010\u5c42\u5bf9\u9f50\uff0c\u518d\u628a\u4e24\u6761\u8fc7\u6ee4\u6761\u4ef6\u62c6\u5f00\u8ba1\u6570\u3002<\/p>\n

\u6211\u4eec\u7528 ArchR \u4f5c\u8005\u63d0\u4f9b\u7684\u4e00\u5bf9\u5c0f\u6587\u4ef6\u505a\u8fd9\u4e2a\u68c0\u67e5\u3002\u7247\u6bb5\u6587\u4ef6\u91cc\u6709 150 \u4e2a\u4e0d\u540c\u6761\u7801\uff0c\u793a\u4f8b Arrow \u4e2d\u80fd\u8bfb\u5230 127 \u4e2a\u6761\u7801\u3002\u5bf9\u540e\u8005\u518d\u5e94\u7528\u4e00\u7ec4\u6559\u5b66\u7528\u95e8\u69db\uff0c\u7559\u4e0b 86 \u4e2a\u3002\u4e0b\u6587\u65e2\u80fd\u590d\u7b97\u8fd9\u4e09\u4e2a\u6570\uff0c\u4e5f\u80fd\u56de\u7b54\u7b2c\u4e09\u4e2a\u6570\u600e\u4e48\u53d8\u6765\u7684\u3002\u8fd9\u4e2a\u5c0f\u6587\u4ef6\u53ea\u542b\u4e24\u6761\u67d3\u8272\u4f53\u4e0a\u7684\u7247\u6bb5\uff0c\u9002\u5408\u89c2\u5bdf\u6570\u636e\u7ed3\u6784\u548c\u8ba1\u6570\u903b\u8f91\u3002ArchR \u5b98\u65b9\u6d4b\u8bd5\u6587\u4ef6<\/a><\/p>\n

\u5148\u5bf9\u9f50\u7247\u6bb5\u6587\u4ef6\u548c Arrow \u7684\u6761\u7801<\/h2>\n

\u5728\u540c\u4e00\u4e2a\u76ee\u5f55\u4e2d\u51c6\u5907 PBSmall.tsv.gz<\/code> \u548c PBSmall.arrow<\/code>\u3002\u4e0b\u9762\u4ee3\u7801\u4f1a\u4e0b\u8f7d\u56fa\u5b9a\u7248\u672c\u7684\u5b98\u65b9\u6d4b\u8bd5\u6587\u4ef6\uff0c\u4f7f\u7528 Bioconductor \u7684 rhdf5<\/code> \u8bfb\u53d6\u5df2\u7ecf\u751f\u6210\u7684 Arrow\u3002\u53ea\u9700\u63d0\u53d6\u51e0\u5217\u5143\u6570\u636e\u5c31\u80fd\u6838\u67e5\u8fd9\u4e2a\u4f8b\u5b50\uff0c\u65e0\u987b\u5148\u5efa\u7acb\u5b8c\u6574\u7684 ArchR \u9879\u76ee\u3002\u672c\u6587\u4f7f\u7528 R 4.5.2\u3001rhdf5 2.54.1\u3002\u793a\u4f8b\u6587\u4ef6\u5185\u90e8\u8bb0\u5f55\u7684 ArchR \u7248\u672c\u4e3a 1.0.2\u3002rhdf5 \u4f7f\u7528\u8bf4\u660e<\/a><\/p>\n

library(rhdf5)\nbase <- paste0(\"https:\/\/raw.githubusercontent.com\/GreenleafLab\/ArchR\/\",\n               \"6feec354ad6c8052ddbc4626a2ca2d858ed465bf\/inst\/testdata\/\")\nfor (nm in c(\"PBSmall.tsv.gz\", \"PBSmall.arrow\")) {\n  if (!file.exists(nm)) download.file(paste0(base, nm), nm, mode = \"wb\")\n}\nfrag <- read.delim(gzfile(\"PBSmall.tsv.gz\"), header = FALSE,\n                   col.names = c(\"chr\", \"start\", \"end\", \"barcode\", \"support\"))\nget_qc <- function(k) as.vector(h5read(\"PBSmall.arrow\", paste0(\"Metadata\/\", k)))\nqc <- data.frame(cell = get_qc(\"CellNames\"), nFrags = get_qc(\"nFrags\"),\n                 TSS = get_qc(\"TSSEnrichment\"))\nstopifnot(!anyDuplicated(qc$cell), all(is.finite(qc$nFrags)),\n          all(is.finite(qc$TSS)))\nraw_ids <- unique(frag$barcode)\nc(fragment_barcodes = length(raw_ids), arrow_cells = nrow(qc),\n  common = length(intersect(raw_ids, qc$cell)))\n<\/code><\/pre>\n
\u8f93\u51fa\u4f9d\u6b21\u4e3a 150\u3001127\u3001127\u3002\u8fd9\u91cc\u539f\u59cb\u6587\u4ef6\u6709 29,399 \u6761\u7247\u6bb5\u8bb0\u5f55\uff0c\u540c\u4e00\u6761\u7801\u53ef\u6709\u8bb8\u591a\u884c\uff0c\u76f4\u63a5\u6570\u884c\u5f97\u5230\u7684\u662f\u7247\u6bb5\u8bb0\u5f55\u6570\u3002Arrow \u7684 127 \u4e2a\u6761\u7801\u5168\u90e8\u80fd\u5728\u8f93\u5165\u540d\u5355\u627e\u5230\uff0c\u5269\u4f59 23 \u4e2a\u6761\u7801\u6ca1\u6709\u5bf9\u5e94\u7684 Arrow \u8d28\u63a7\u503c\u3002\u7531\u8fd9\u4e24\u4e2a\u6587\u4ef6\u53ef\u4ee5\u5b9a\u4f4d\u5dee\u5f02\u53d1\u751f\u5728\u6700\u7ec8\u4e8c\u6b21\u7b5b\u9009\u4e4b\u524d\u3002\u8981\u67e5\u67d0\u4e00\u4e2a\u7f3a\u5931\u6761\u7801\u7684\u539f\u56e0\uff0c\u8fd8\u9700\u8981\u5efa\u6863\u65f6\u7684\u53c2\u6570\u3001\u5141\u8bb8\u8fdb\u5165\u7684\u6761\u7801\u540d\u5355\u548c\u65e5\u5fd7\u3002\u628a\u8fd9 23 \u4e2a\u76f4\u63a5\u767b\u8bb0\u4e3a\u201cTSS \u4e0d\u5408\u683c\u201d\u4f1a\u7ed9\u540e\u7eed\u6392\u67e5\u6307\u9519\u65b9\u5411\u3002<\/p>\n
\u5728\u591a\u6837\u672c\u9879\u76ee\u91cc\u5bf9\u6761\u7801\u65f6\u8fd8\u8981\u4fdd\u7559\u6837\u672c\u8eab\u4efd\u3002\u4e24\u4e2a\u6587\u5e93\u5b8c\u5168\u53ef\u80fd\u90fd\u51fa\u73b0\u540c\u4e00\u4e32 10x \u6761\u7801\u3002\u82e5\u9879\u76ee\u5bfc\u51fa\u7684\u7ec6\u80de\u540d\u5e26\u6709\u6837\u672c\u524d\u7f00\uff0c\u5148\u6309\u6587\u5e93\u5efa\u5bf9\u5e94\u5173\u7cfb\uff0c\u518d\u5728\u5404\u6587\u5e93\u5185\u90e8\u6bd4\u8f83\u6761\u7801\u3002\u4e0d\u52a0\u533a\u5206\u5730\u5220\u9664\u6240\u6709\u524d\u7f00\u518d\u53d6\u4ea4\u96c6\uff0c\u4f1a\u8ba9\u53e6\u4e00\u4e2a\u6587\u5e93\u4e2d\u7684\u540c\u540d\u6761\u7801\u770b\u8d77\u6765\u50cf\u662f\u627e\u56de\u4e86\u4e22\u5931\u7684\u7ec6\u80de\u3002<\/p>\n
\u4e24\u4e2a\u6307\u6807\u56de\u7b54\u7684\u662f\u4e24\u4ef6\u4e0d\u540c\u7684\u4e8b<\/h2>\n
nFrags<\/code> \u63cf\u8ff0\u6bcf\u4e2a\u7ec6\u80de\u53ef\u7528\u7684\u6838\u7247\u6bb5\u6570\u91cf\u3002\u7247\u6bb5\u5f88\u5c11\u65f6\uff0c\u5373\u4f7f\u7ec6\u80de\u6709\u6e05\u6670\u7684\u542f\u52a8\u5b50\u4fe1\u53f7\uff0c\u8bb8\u591a\u8c03\u63a7\u533a\u57df\u4ecd\u53ef\u80fd\u91c7\u6837\u4e0d\u8db3\u3002TSSEnrichment<\/code> \u53cd\u6620\u8f6c\u5f55\u8d77\u59cb\u4f4d\u70b9\u9644\u8fd1\u7684\u63d2\u5165\u4fe1\u53f7\u76f8\u5bf9\u4e8e\u4e24\u4fa7\u80cc\u666f\u7684\u5bcc\u96c6\u3002\u4e00\u4e2a\u6761\u7801\u53ef\u4ee5\u79ef\u7d2f\u5f88\u591a\u7247\u6bb5\uff0c\u4f46\u5982\u679c\u8fd9\u4e9b\u7247\u6bb5\u5728\u8d77\u59cb\u4f4d\u70b9\u9644\u8fd1\u6ca1\u6709\u5f62\u6210\u6e05\u6670\u7684\u5bcc\u96c6\uff0c\u5c31\u9700\u8981\u56de\u770b\u80cc\u666f\u4fe1\u53f7\u548c\u6ce8\u91ca\u3002\u4e24\u4e2a\u6307\u6807\u8054\u5408\u4f7f\u7528\uff0c\u624d\u80fd\u533a\u5206\u201c\u4fe1\u606f\u91cf\u6709\u9650\u201d\u548c\u201c\u7247\u6bb5\u4e0d\u5c11\u4f46\u4fe1\u53f7\u4e0e\u80cc\u666f\u96be\u4ee5\u5206\u5f00\u201d\u3002ArchR \u5bf9\u9010\u7ec6\u80de\u8d28\u63a7\u6307\u6807\u7684\u5b9a\u4e49<\/a><\/p>\n
\u672c\u4f8b\u6709\u610f\u7528 nFrags >= 150<\/code>\u3001TSS >= 5<\/code> \u5bf9\u73b0\u6709 127 \u884c\u505a\u4e00\u6b21\u4e8c\u6b21\u7b5b\u9009\u3002150 \u53ea\u662f\u8ba9\u8fd9\u4e2a\u88c1\u526a\u8fc7\u7684\u5c0f\u6587\u4ef6\u51fa\u73b0\u56db\u79cd\u60c5\u51b5\uff0c\u4e0d\u80fd\u76f4\u63a5\u7528\u4e8e\u5b8c\u6574\u6587\u5e93\u3002\u6700\u7b80\u5355\u7684\u8bca\u65ad\u662f\u4fdd\u7559\u4e24\u5217\u771f\u5047\u503c\uff0c\u505a\u4e00\u5f20\u4e8c\u7ef4\u8ba1\u6570\u8868\u3002\u5982\u679c\u63a5\u8fde\u7b5b\u4e24\u6b21\u53ea\u4fdd\u7559\u6700\u540e\u7684\u884c\u6570\uff0c\u5c31\u4f1a\u4e22\u6389\u4e24\u6761\u6761\u4ef6\u91cd\u53e0\u7684\u4fe1\u606f\u3002<\/p>\n
frag_ok <- qc$nFrags >= 150\ntss_ok <- qc$TSS >= 5\ntable(nFrags_pass = factor(frag_ok, levels = c(FALSE, TRUE)),\n      TSS_pass = factor(tss_ok, levels = c(FALSE, TRUE)))\nc(total = nrow(qc), kept = sum(frag_ok & tss_ok),\n  fails_either = sum(!frag_ok | !tss_ok))\n<\/code><\/pre>\n
\n\n\n\n\n\n\n\n
\u5728\u8fd9 127 \u4e2a\u6761\u7801\u4e2d<\/th>\nTSS \u672a\u8fbe 5<\/th>\nTSS \u8fbe\u5230 5<\/th>\n\u5408\u8ba1<\/th>\n<\/tr>\n<\/thead>\n
\u6838\u7247\u6bb5\u6570\u672a\u8fbe 150<\/td>\n23<\/td>\n13<\/td>\n36<\/td>\n<\/tr>\n
\u6838\u7247\u6bb5\u6570\u8fbe\u5230 150<\/td>\n5<\/td>\n86<\/td>\n91<\/td>\n<\/tr>\n
\u5408\u8ba1<\/td>\n28<\/td>\n99<\/td>\n127<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"ArchR
\u5728\u5b98\u65b9\u5c0f\u6587\u4ef6\u5df2\u6709\u7684 127 \u4e2a\u6761\u7801\u4e0a\u505a\u4e8c\u6b21\u7b5b\u9009\u3002\u56db\u683c\u4e92\u65a5\uff0c23 \u4e2a\u4e24\u9879\u5747\u672a\u8fbe\u6807\u7684\u6761\u7801\u4e0e\u672a\u8fdb\u5165 Arrow \u7684 23 \u4e2a\u6761\u7801\u6765\u81ea\u4e0d\u540c\u96c6\u5408\u3002<\/figcaption><\/figure>\n
\u5982\u679c\u5148\u6309\u7247\u6bb5\u6570\u7b5b\uff0c127 \u4e2a\u6761\u7801\u91cc\u5269 91 \u4e2a\uff0c\u8fd9\u65f6\u63d0\u9ad8 TSS \u8981\u6c42\u53c8\u6392\u9664 5 \u4e2a\u3002\u5982\u679c\u5148\u6309 TSS \u7b5b\uff0c\u4f1a\u5148\u5269 99 \u4e2a\uff0c\u518d\u6392\u9664 13 \u4e2a\u3002\u6700\u540e\u90fd\u662f 86 \u4e2a\u3002\u4e24\u79cd\u987a\u5e8f\u7684\u4e2d\u95f4\u6570\u5b57\u4e0d\u540c\uff0c\u662f\u56e0\u4e3a 23 \u4e2a\u6761\u7801\u540c\u65f6\u672a\u8fbe\u4e24\u9879\u8981\u6c42\u3002\u5199\u8d28\u63a7\u8bb0\u5f55\u65f6\uff0c\u53ef\u4ee5\u7528\u201c\u4ec5\u7247\u6bb5\u6570\u4e0d\u8db3\u201d\u201c\u4ec5 TSS \u4e0d\u8db3\u201d\u201c\u4e24\u9879\u90fd\u4e0d\u8db3\u201d\u4e09\u4e2a\u4e92\u65a5\u539f\u56e0\uff0c\u5206\u522b\u586b 13\u30015\u300123\u3002\u8bfb\u8005\u65e2\u80fd\u590d\u7b97\u5408\u8ba1\u5254\u9664\u7684 41 \u4e2a\uff0c\u4e5f\u80fd\u770b\u61c2\u7a76\u7adf\u662f\u54ea\u6761\u8fb9\u754c\u503c\u5f97\u4ed4\u7ec6\u68c0\u67e5\u3002\u8fd9\u91cc\u4e24\u9879\u90fd\u4e0d\u8db3\u7684 23 \u4e2a\u4ecd\u4f4d\u4e8e Arrow \u5185\uff0c\u4e0e\u524d\u9762\u5b8c\u5168\u6ca1\u6709\u8fdb\u5165 Arrow \u7684 23 \u4e2a\u662f\u4e0d\u540c\u7684\u6761\u7801\u3002<\/p>\n
\u628a\u8fd9\u5f20\u8868\u79fb\u5230\u81ea\u5df1\u7684 ArchR \u9879\u76ee<\/h2>\n
\u5df2\u6709\u9879\u76ee\u53ef\u4ee5\u901a\u8fc7\u516c\u5f00\u63a5\u53e3 getCellColData()<\/code> \u63d0\u53d6\u5f53\u524d\u7ec6\u80de\u7684\u8d28\u63a7\u5217\u3002\u4e0b\u9762\u5047\u8bbe\u4f60\u7684\u9879\u76ee\u5bf9\u8c61\u540d\u4e3a proj<\/code>\u3002\u5148\u7edf\u8ba1\u6bcf\u4e2a\u6837\u672c\u5f53\u524d\u53ef\u89c1\u7684\u7ec6\u80de\u6570\uff0c\u518d\u770b\u4e2d\u4f4d\u6570\u548c\u56db\u5206\u4f4d\u6570\u3002\u540c\u4e00\u4e2a\u5408\u5e76\u6563\u70b9\u56fe\u91cc\uff0c\u5982\u679c\u4e00\u4e2a\u5927\u6587\u5e93\u5360\u4e86\u7edd\u5927\u591a\u6570\u70b9\uff0c\u5c0f\u6587\u5e93\u6574\u4f53\u7684\u4f4d\u79fb\u5f88\u5bb9\u6613\u88ab\u906e\u4f4f\u3002ArchR \u9879\u76ee\u6570\u636e\u63d0\u53d6\u63a5\u53e3<\/a><\/p>\n
md <- as.data.frame(ArchR::getCellColData(\n  proj, select = c(\"Sample\", \"nFrags\", \"TSSEnrichment\")))\nprint(table(md$Sample))\nby(md, md$Sample, function(d) {\n  rbind(nFrags = quantile(d$nFrags, c(.25, .5, .75), na.rm = TRUE),\n        TSS = quantile(d$TSSEnrichment, c(.25, .5, .75), na.rm = TRUE))\n})\n<\/code><\/pre>\n
\u5982\u679c\u67d0\u4e2a\u6837\u672c\u6574\u4f53\u6838\u7247\u6bb5\u504f\u5c11\uff0c\u5148\u770b\u8f93\u5165\u7684\u6709\u6548\u7247\u6bb5\u3001\u6d4b\u5e8f\u8986\u76d6\u548c\u7247\u6bb5\u957f\u5ea6\u5206\u5e03\u3002\u5982\u679c\u6838\u7247\u6bb5\u4e0d\u5c11\u800c\u6574\u6279\u7684 TSS \u5206\u5e03\u90fd\u504f\u4f4e\uff0c\u5148\u6838\u5bf9\u6bd4\u5bf9\u53c2\u8003\u7ec4\u88c5\u3001\u67d3\u8272\u4f53\u547d\u540d\u4ee5\u53ca\u8ba1\u7b97\u5bcc\u96c6\u4f7f\u7528\u7684\u8d77\u59cb\u4f4d\u70b9\u6ce8\u91ca\uff0c\u518d\u770b\u8be5\u6587\u5e93\u7684\u805a\u5408 TSS \u66f2\u7ebf\u3002\u82e5\u53ea\u6709\u5c11\u6570\u70b9\u5904\u5728\u7b5b\u9009\u8fb9\u7f18\uff0c\u53ef\u5355\u72ec\u67e5\u770b\u5b83\u4eec\u5728\u540e\u7eed\u964d\u7ef4\u4e2d\u7684\u4f4d\u7f6e\uff0c\u4ee5\u53ca\u9608\u503c\u8f7b\u5fae\u53d8\u5316\u540e\u76ee\u6807\u7fa4\u7684\u6210\u5458\u662f\u5426\u660e\u663e\u6539\u53d8\u3002\u5355\u9760\u4e00\u4e2a\u4f4e\u5206\u65e0\u6cd5\u533a\u5206\u6587\u5e93\u8d28\u91cf\u3001\u6ce8\u91ca\u9519\u914d\u4e0e\u7ec6\u80de\u672c\u8eab\u7684\u5dee\u5f02\u3002<\/p>\n
\u8fd8\u8981\u8bb0\u4f4f\u8fd9\u5f20\u8868\u7684\u8d77\u70b9\u3002\u9879\u76ee\u5bf9\u8c61\u53ea\u542b\u5f53\u524d\u7eb3\u5165\u7684\u7ec6\u80de\uff0c\u4e4b\u540e\u653e\u5bbd\u7b5b\u9009\u53ea\u80fd\u627e\u56de\u4ecd\u6709\u8bb0\u5f55\u7684\u6761\u7801\u3002\u82e5\u9700\u8981\u91cd\u65b0\u8bc4\u4f30\u5efa\u6863\u9636\u6bb5\u6392\u9664\u7684\u6761\u7801\uff0c\u5e94\u56de\u5230\u6bcf\u4e2a\u6837\u672c\u5bf9\u5e94\u7684 fragments \u6587\u4ef6\uff0c\u6838\u5bf9\u6392\u5e8f\u3001bgzip \u538b\u7f29\u3001\u53c2\u8003\u57fa\u56e0\u7ec4\u4e0e createArrowFiles()<\/code> \u5f53\u65f6\u4f7f\u7528\u7684\u95e8\u69db\u3002\u5728\u72ec\u7acb\u76ee\u5f55\u91cd\u5efa\u4e00\u4efd\u53ef\u6bd4\u8f83\u7684 Arrow\uff0c\u4fdd\u5b58\u539f\u59cb\u7ed3\u679c\u548c\u53c2\u6570\uff0c\u518d\u9010\u6761\u7801\u505a\u5dee\u96c6\u3002\u6700\u540e\u4ea4\u4ed8\u6bcf\u4e2a\u6587\u5e93\u7684\u8f93\u5165\u6761\u7801\u6570\u3001\u5165\u6863\u6570\u3001\u6700\u7ec8\u4fdd\u7559\u6570\u53ca\u4e24\u9879\u6307\u6807\u7684\u4ea4\u53c9\u8868\uff0c\u540c\u4e8b\u5c31\u80fd\u6cbf\u539f\u8def\u7ebf\u6838\u67e5\u4e00\u6b21\u3002createArrowFiles \u53c2\u6570\u8bf4\u660e<\/a><\/p>\n
\u628a\u95e8\u69db\u632a\u4e00\u5c0f\u6b65\uff0c\u5b9e\u9645\u589e\u52a0\u7684\u662f\u54ea\u4e9b\u6761\u7801\uff1f<\/h2>\n
\u5bf9\u540c\u4e00\u4efd Arrow\uff0c\u53ef\u4ee5\u56fa\u5b9a\u4e00\u4e2a\u6307\u6807\uff0c\u53ea\u79fb\u52a8\u53e6\u4e00\u4e2a\u3002\u4ee5\u7247\u6bb5\u6570\u4e00\u767e\u4e94\u5341\u3001\u5bcc\u96c6\u5206\u4e94\u4e3a\u57fa\u7ebf\uff0c\u4fdd\u7559\u516b\u5341\u516d\u4e2a\u6761\u7801\u3002\u5c06\u7247\u6bb5\u6570\u8981\u6c42\u964d\u5230\u4e00\u767e\u800c\u4fdd\u6301\u5bcc\u96c6\u5206\u4e0d\u53d8\uff0c\u4fdd\u7559\u4e5d\u5341\u4e5d\u4e2a\u3002\u628a\u7247\u6bb5\u6570\u5347\u5230\u4e24\u767e\uff0c\u4fdd\u7559\u56db\u5341\u4e5d\u4e2a\u3002\u518d\u628a\u7247\u6bb5\u95e8\u69db\u6062\u590d\u5230\u4e00\u767e\u4e94\u5341\uff0c\u5206\u522b\u628a\u5bcc\u96c6\u5206\u8bbe\u4e3a\u56db\u548c\u516d\uff0c\u4fdd\u7559\u6570\u4e3a\u4e5d\u5341\u4e00\u548c\u4e03\u5341\u4e8c\u3002\u4ee5\u4e0b\u4ee3\u7801\u76f4\u63a5\u4ece\u4e0a\u6587\u7684\u6570\u636e\u6846\u8ba1\u7b97\u3002\u628a\u4e24\u4e2a\u95e8\u69db\u4e00\u6b21\u53ea\u52a8\u4e00\u4e2a\uff0c\u624d\u80fd\u770b\u6e05\u54ea\u4e9b\u53d8\u5316\u6765\u81ea\u7247\u6bb5\u91cf\uff0c\u54ea\u4e9b\u6765\u81ea\u8d77\u59cb\u4f4d\u70b9\u4fe1\u53f7\u3002<\/p>\n
grid <- data.frame(frag = c(100, 150, 200, 150, 150), tss = c(5, 5, 5, 4, 6))\ngrid$kept <- mapply(function(f, t) sum(qc$nFrags >= f & qc$TSS >= t),\n                    grid$frag, grid$tss)\nprint(grid)\nrescued <- subset(qc, nFrags >= 100 & nFrags < 150 & TSS >= 5)\nstopifnot(nrow(rescued) == 13)\n<\/code><\/pre>\n
\u8fd9\u4e9b\u589e\u52a0\u7684\u6761\u7801\u503c\u5f97\u5355\u72ec\u4fdd\u5b58\u3002\u4f8b\u5982\u653e\u5bbd\u7247\u6bb5\u8981\u6c42\u65f6\u627e\u56de\u7684\u5341\u4e09\u4e2a\uff0c\u5168\u90fd\u8de8\u8fc7\u4e86\u5bcc\u96c6\u5206\u95e8\u69db\uff0c\u53ef\u4ee5\u9010\u6761\u67e5\u770b\u7247\u6bb5\u957f\u5ea6\u3001\u68c0\u6d4b\u5230\u7684\u5f00\u653e\u533a\u57df\uff0c\u4ee5\u53ca\u8fd9\u4e9b\u6761\u7801\u5728\u540c\u4e00\u4e2a\u6587\u5e93\u4e2d\u7684\u5206\u5e03\u4f4d\u7f6e\u3002\u53cd\u8fc7\u6765\uff0c\u4ece\u4e00\u767e\u4e94\u5341\u63d0\u9ad8\u5230\u4e24\u767e\u6240\u51cf\u5c11\u7684\u4e09\u5341\u4e03\u4e2a\u6761\u7801\u90fd\u6709\u8fbe\u6807\u7684\u8d77\u59cb\u4f4d\u70b9\u4fe1\u53f7\u3002\u82e5\u67d0\u7c7b\u7a00\u5c11\u7ec6\u80de\u6070\u597d\u96c6\u4e2d\u5728\u8fd9\u4e2a\u6df1\u5ea6\u533a\u95f4\uff0c\u95e8\u69db\u4f1a\u8fde\u5e26\u6539\u53d8\u5b83\u7684\u89c2\u5bdf\u9891\u7387\u3002\u8981\u5224\u65ad\u662f\u5426\u786e\u6709\u8fd9\u79cd\u60c5\u51b5\uff0c\u9700\u8981\u72ec\u7acb\u6807\u8bb0\u6216\u540e\u7eed\u6ce8\u91ca\u6765\u6838\u5bf9\u3002\u672c\u4f8b\u53ea\u5c55\u793a\u54ea\u4e9b\u6761\u7801\u53d7\u8fb9\u754c\u5f71\u54cd\uff0c\u4e0d\u80fd\u4ece\u6761\u7801\u540d\u79f0\u731c\u6d4b\u7ec4\u7ec7\u6210\u5206\u3002<\/p>\n
\u5b9e\u9645\u9879\u76ee\u6700\u597d\u628a\u6bcf\u4e2a\u6587\u5e93\u7684\u654f\u611f\u6027\u8868\u505a\u6210\u76f8\u540c\u7684\u884c\u5217\uff0c\u7136\u540e\u540c\u65f6\u62a5\u544a\u7edd\u5bf9\u6570\u4e0e\u6bd4\u4f8b\u3002\u7532\u6587\u5e93\u4ece\u4e00\u4e07\u4e2a\u7ec6\u80de\u589e\u52a0\u4e94\u5341\u4e2a\uff0c\u4e59\u6587\u5e93\u4ece\u4e00\u767e\u4e2a\u589e\u52a0\u4e94\u5341\u4e2a\uff0c\u7edd\u5bf9\u6570\u770b\u8d77\u6765\u4e00\u6837\uff0c\u5f71\u54cd\u5374\u5b8c\u5168\u4e0d\u540c\u3002\u628a\u4e24\u8005\u5408\u5e76\u518d\u8ba1\u7b97\u6bd4\u4f8b\u4f1a\u8ba9\u6df1\u5ea6\u8f83\u5927\u7684\u7532\u6587\u5e93\u63a9\u76d6\u4e59\u6587\u5e93\u7684\u53d8\u5316\u3002\u5982\u679c\u4e0d\u540c\u6761\u4ef6\u7531\u4e0d\u540c\u6279\u6b21\u5b8c\u6210\uff0c\u8fd8\u53ef\u5728\u6837\u672c\u8868\u4e2d\u5217\u51fa\u6bcf\u4e2a\u6761\u4ef6\u5bf9\u5e94\u7684\u5efa\u5e93\u65e5\u671f\u548c\u5904\u7406\u65b9\u5f0f\u3002\u67d0\u4e00\u6761\u4ef6\u7684\u4fdd\u7559\u7387\u59cb\u7ec8\u504f\u4f4e\u65f6\uff0c\u5148\u67e5\u6761\u4ef6\u548c\u6279\u6b21\u6709\u6ca1\u6709\u5206\u5f00\u5b89\u6392\uff0c\u518d\u8ba8\u8bba\u7ec6\u80de\u672c\u8eab\u7684\u67d3\u8272\u8d28\u72b6\u6001\u3002<\/p>\n
\u4ece\u4e8c\u7ef4\u8ba1\u6570\u56de\u5230\u7247\u6bb5\u4fe1\u53f7<\/h2>\n
\u5f53\u4e00\u4e2a\u6587\u5e93\u6574\u4f53\u5bcc\u96c6\u5206\u504f\u4f4e\u65f6\uff0c\u53ef\u518d\u753b\u805a\u5408\u8d77\u59cb\u4f4d\u70b9\u66f2\u7ebf\u3002\u9009\u62e9\u4e0e\u6bd4\u5bf9\u53c2\u8003\u4e00\u81f4\u7684\u8d77\u59cb\u4f4d\u70b9\u6ce8\u91ca\uff0c\u628a\u63d2\u5165\u4fe1\u53f7\u6309\u76f8\u5bf9\u4f4d\u7f6e\u6c47\u603b\uff0c\u89c2\u5bdf\u4e2d\u5fc3\u662f\u5426\u6709\u5cf0\u3001\u4e24\u4fa7\u80cc\u666f\u662f\u5426\u5747\u5300\u3002\u4e0d\u540c\u6587\u5e93\u5e76\u6392\u5c55\u793a\u65f6\u6cbf\u7528\u540c\u4e00\u5957\u7a97\u53e3\u4e0e\u5f52\u4e00\u5316\u65b9\u5f0f\u3002\u5047\u5982\u4e00\u4efd\u6587\u5e93\u66f2\u7ebf\u770b\u8d77\u6765\u51e0\u4e4e\u5e73\u5766\uff0c\u5148\u6838\u5bf9\u6ce8\u91ca\u548c\u7247\u6bb5\u80fd\u5426\u5728\u76f8\u540c\u67d3\u8272\u4f53\u4e0a\u5bf9\u9f50\uff0c\u518d\u67e5\u7ec6\u80de\u7b5b\u9009\u7684\u5148\u540e\u987a\u5e8f\u3002\u82e5\u5728\u5408\u5e76\u56fe\u4e0a\u753b\u7684\u662f\u5168\u4f53\u6761\u7801\uff0c\u800c\u5355\u7ec6\u80de\u7edf\u8ba1\u6765\u81ea\u4e25\u683c\u7b5b\u9009\u540e\u7684\u5b50\u96c6\uff0c\u4e24\u8005\u4f1a\u663e\u793a\u4e0d\u540c\u7684\u4fe1\u53f7\u5f3a\u5ea6\u3002<\/p>\n
\u4ea4\u4ed8\u7ed9\u5408\u4f5c\u8005\u65f6\uff0c\u7ed9\u6bcf\u4e2a\u6587\u5e93\u4e00\u5f20\u6761\u7801\u7ea7\u7ed3\u679c\u8868\u4f1a\u6bd4\u53ea\u5b58\u6700\u7ec8\u901a\u8fc7\u540d\u5355\u66f4\u65b9\u4fbf\u3002\u7528\u4e00\u5217\u4fdd\u5b58\u8f93\u5165\u540d\uff0c\u4e00\u5217\u4fdd\u5b58\u9879\u76ee\u4e2d\u7684\u5e26\u6837\u672c\u540d\u524d\u7f00\u7684\u540d\u5b57\uff0c\u540c\u65f6\u4fdd\u5b58\u539f\u59cb\u7247\u6bb5\u6570\u3001\u5bcc\u96c6\u5206\u548c\u4e24\u4e2a\u72ec\u7acb\u7684\u901a\u8fc7\u6807\u8bb0\u3002\u4e0a\u6e38\u5df2\u7b5b\u6389\u3001\u65e0\u6cd5\u53d6\u5f97\u5bcc\u96c6\u5206\u7684\u6761\u7801\uff0c\u5728\u8fd9\u4e00\u5217\u7559\u7f3a\u5931\u5e76\u6ce8\u660e\u6765\u6e90\u3002\u540e\u7eed\u82e5\u8981\u91cd\u5b9a\u95e8\u69db\uff0c\u540c\u4e8b\u53ef\u4ee5\u4ece\u8868\u4e2d\u76f4\u63a5\u91cd\u5f97\u56db\u683c\u8ba1\u6570\uff0c\u5e76\u6311\u51fa\u8981\u518d\u68c0\u67e5\u7684\u6761\u7801\u3002\u771f\u6b63\u9700\u8981\u91cd\u65b0\u8fd0\u884c\u4e0a\u6e38\u5efa\u6863\u7684\u60c5\u51b5\u4e5f\u4f1a\u4e00\u76ee\u4e86\u7136\u3002<\/p>\n
\u4e0b\u8f7d\u4ee3\u7801\u548c\u793a\u4f8b\u6570\u636e\uff0c\u5728 Linux \u4e0a\u590d\u73b0<\/h2>\n
\u4e0b\u8f7d\u672c\u7bc7 R \u4ee3\u7801\uff08ZIP\uff0c4.0 KiB\uff09<\/a> \u00b7 \u4e0b\u8f7d\u914d\u5957\u793a\u4f8b\u6570\u636e\uff08ZIP\uff0c836.5 KiB\uff09<\/a><\/p>\n
\u5c06\u4e24\u4e2a ZIP \u89e3\u538b\u5230\u540c\u4e00\u4f4d\u7f6e\uff0c\u8fdb\u5165 027-archr<\/code> \u76ee\u5f55\uff0c\u8fd0\u884c Rscript --vanilla run.R<\/code>\u3002\u6253\u5f00 results\/metrics.tsv<\/code> \u67e5\u770b\u7ed3\u679c\uff0c\u4ee3\u7801\u5305\u4e2d\u7684 expected\/metrics.tsv<\/code> \u53ef\u4f9b\u9010\u884c\u6838\u5bf9\u3002<\/p>\n
\u672c\u6b21\u4ece\u4e0b\u8f7d\u5305\u590d\u73b0\u7684\u6b65\u9aa4\u662f\u201c\u7528 rhdf5 \u4ece\u4f5c\u8005\u7684 Arrow \u4e0e\u7247\u6bb5\u6838\u5bf9\u8fc7\u6ee4\u7ed3\u679c\u201d\u3002Linux x86_64\u3001R 4.3.3\u3001rhdf5 2.40.0 \u7684\u8f93\u51fa\u4e3a\u7247\u6bb5\u6587\u4ef6\u6761\u7801 150\uff0cArrow \u7ec6\u80de 127\uff0c\u4e24\u9879\u8d28\u63a7\u901a\u8fc7 86\u3002<\/p>\n
\u4e0b\u8f7d\u7248\u53e6\u5b58 arrow-qc.csv\u3002\u628a TSS \u5bcc\u96c6\u548c\u7247\u6bb5\u6570\u5206\u522b\u8bbe\u4e3a\u901a\u8fc7\u6807\u8bb0\uff0c\u518d\u53d6\u4e24\u4e2a\u6807\u8bb0\u7684\u4ea4\u96c6\u3002\u53ea\u6709 Arrow \u4e2d\u7684\u6761\u7801\u6709\u8fd9\u4e24\u9879\u53ef\u4f9b\u7edf\u8ba1\u3002\u539f\u7247\u6bb5\u6587\u4ef6\u4e2d\u672a\u5199\u5165 Arrow \u7684\u6761\u7801\u5e94\u4fdd\u7559\u5728\u53e6\u4e00\u5f20\u6e05\u5355\u4e2d\u3002<\/p>\n
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