{"id":27751,"date":"2024-02-02T16:25:37","date_gmt":"2024-02-02T08:25:37","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=27751"},"modified":"2024-02-02T16:25:38","modified_gmt":"2024-02-02T08:25:38","slug":"scmerge2%e9%ad%94%e6%b3%95%e6%8c%87%e5%8d%97%ef%bc%9a%e5%b0%8f%e6%9e%9c%e5%b8%a6%e4%bd%a0%e9%a2%86%e7%95%a5%e5%8d%95%e7%bb%86%e8%83%9e%e6%95%b0%e6%8d%ae%e8%9e%8d%e5%90%88%e7%9a%84%e5%a5%87%e5%a6%99","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=27751","title":{"rendered":"scMerge2\u9b54\u6cd5\u6307\u5357\uff1a\u5c0f\u679c\u5e26\u4f60\u9886\u7565\u5355\u7ec6\u80de\u6570\u636e\u878d\u5408\u7684\u5947\u5999\u4e4b\u65c5\uff01"},"content":{"rendered":"

\u524d\u8a00<\/strong><\/p>\n

\u5355\u7ec6\u80de\u591a\u6837\u672c\u6574\u5408\u5de5\u5177\u5927\u5bb6\u4e5f\u5b66\u8fc7\u5f88\u591a\u4e86\u5427\uff01\u4f46\u662f\u9664\u4e86 Seurat\u3001SAUCIE \u548c Scanorama \u4e4b\u5916\uff0c\u5176\u4ed6\u51e0\u79cd\u5feb\u901f\u7a0b\u5e8f\uff08deepMNN\u3001BBKNN\u3001Harmony\u3001scVI\u3001scANVI \u548c DESC\uff09\u90fd\u4fa7\u91cd\u4e8e\u63d0\u53d6\u8054\u5408\u5d4c\u5165\uff0c\u800c\u4e0d\u8fd4\u56de\u8c03\u6574\u540e\u7684\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u3002\u968f\u7740\u5bf9\u6837\u672c\u6c34\u5e73\u5206\u6790\u7684\u9700\u6c42\u65e5\u76ca\u589e\u957f\uff0c\u7f3a\u4e4f\u8c03\u6574\u540e\u7684\u8868\u8fbe\u77e9\u9635\u9650\u5236\u4e86\u6b64\u7c7b\u7efc\u5408\u7ed3\u679c\u7684\u5229\u7528\uff0c\u524a\u5f31\u4e86\u5176\u6709\u6548\u6027\u548c\u666e\u9002\u6027\u3002\u56e0\u6b64\uff0c\u4e0b\u4e00\u4ee3\u56fe\u96c6\u7ea7\u6574\u5408\u7b97\u6cd5\u5e94\u80fd\u6574\u5408\u5927\u91cf\u7814\u7a76\uff0c\u751f\u6210\u5171\u8bc6\u7ec6\u80de\u7c7b\u578b\u56fe\u548c\u8c03\u6574\u8868\u8fbe\u77e9\u9635\uff0c\u4ee5\u4fbf\u8fdb\u4e00\u6b65\u8fdb\u884c\u4e0b\u6e38\u5206\u6790\u3002\u4e3a\u6b64\uff0c scMerge2\u5e94\u8fd0\u800c\u751f\uff0c\u8fd9\u662f\u4e00\u79cd\u53ef\u6269\u5c55\u7684\u9ad8\u5bb9\u91cf\u7b97\u6cd5\uff0c\u53ef\u5bf9\u56fe\u96c6\u89c4\u6a21\u7684\u591a\u6837\u672c\u591a\u6761\u4ef6\u5355\u7ec6\u80de\u7814\u7a76\u8fdb\u884c\u6570\u636e\u6574\u5408\u3002\u4e0b\u9762\u8ddf\u7740\u5c0f\u679c\u6765\u5b66\u4e60\u4e00\u4e0b\u5427\uff01<\/p>\n

scMerge2\u4ecb\u7ecd<\/strong><\/p>\n

scMerge \u7b97\u6cd5\u53ef\u53bb\u9664\u6279\u6b21\u6548\u5e94\uff0c\u5e76\u5bf9\u5355\u7ec6\u80de RNA-Seq \u6570\u636e\u8fdb\u884c\u5f52\u4e00\u5316\u5904\u7406\u3002\u5b83\u7531\u4e09\u4e2a\u5173\u952e\u90e8\u5206\u7ec4\u6210\uff0c\u5305\u62ec<\/p>\n

\u2022 \u786e\u5b9a\u7a33\u5b9a\u8868\u8fbe\u57fa\u56e0\uff08SEG\uff09\u4f5c\u4e3a “\u9634\u6027\u5bf9\u7167”\uff0c\u4ee5\u4f30\u8ba1\u4e0d\u9700\u8981\u7684\u56e0\u7d20\uff1b<\/p>\n

\u2022 \u6784\u5efa\u4f2a\u91cd\u590d\uff0c\u4ee5\u4f30\u8ba1\u4e0d\u9700\u8981\u7684\u56e0\u7d20\u7684\u5f71\u54cd\uff1b<\/p>\n

\u2022 \u4f7f\u7528\u5feb\u901f RUVIII \u6a21\u578b\u8c03\u6574\u5b58\u5728\u4e0d\u5fc5\u8981\u53d8\u5f02\u7684\u6570\u636e\u96c6\u3002<\/p>\n

<\/p>\n

scMerge2\u793a\u4f8b<\/strong><\/p>\n

\u5b89\u88c5R\u5305<\/strong><\/p>\n

scMerge\u53ef\u5728bioconductor \uff08https:\/\/bioconductor.org\/packages\/scMerge\uff09 \u4e0a\u4f7f\u7528\u3002\u60a8\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u65b9\u6cd5\u5b89\u88c5\u5b83\uff1a<\/p>\n

## \u4ece Bioconductor \u5b89\u88c5 scMerge\uff0c\u9700\u8981 R 3.6.0 \u6216\u4ee5\u4e0a\u7248\u672c<\/p>\n

BiocManager::install(“scMerge”)<\/p>\n

##\u60a8\u4e5f\u53ef\u4ee5\u5c1d\u8bd5\u5b89\u88c5 ScMerge \u7684 Bioconductor \u5f00\u53d1\u7248<\/p>\n

BiocManager::install(“scMerge”, version = “devel”)<\/p>\n

\u52a0\u8f7d\u5305\u548c\u6570\u636e<\/strong><\/p>\n

suppressPackageStartupMessages({<\/p>\n

library(SingleCellExperiment)<\/p>\n

library(scMerge)<\/p>\n

library(scater)<\/p>\n

})<\/p>\n

\u6211\u4eec\u5728R\u5305\u4e2d\u63d0\u4f9b\u4e86\u4e00\u4e2a\u5c0f\u9f20\u80da\u80ce\u5e72\u7ec6\u80de\uff08mESC\uff09\u6570\u636e\u793a\u4f8b\uff0c\u4ee5\u53ca\u4e00\u7ec4\u9884\u5148\u8ba1\u7b97\u597d\u7684\u7a33\u5b9a\u8868\u8fbe\u57fa\u56e0\uff08SEG\uff09\u5217\u8868\uff0c\u7528\u4f5c\u9634\u6027\u5bf9\u7167\u57fa\u56e0\u3002<\/p>\n

\u5b8c\u6574\u7684\u3001\u672a\u7ecf\u89c4\u8303\u5316\u7684 mESC \u6570\u636e\u53ef\u5728\u8fd9\u91cc\u627e\u5230\uff08https:\/\/www.maths.usyd.edu.au\/u\/yingxinl\/wwwnb\/scMergeData\/sce_mESC.rda\uff09\u3002R\u5305\u9644\u5e26\u4e86\u8be5\u6570\u636e\u7684\u5b50\u6837\u672c\u3001\u4e24\u4e2a\u6279\u6b21\u7248\u672c\uff08\u547d\u540d\u4e3a\u201cbatch2\u201d\u548c\u201cbatch3\u201d\uff0c\u4ee5\u4fbf\u4e0e\u5b8c\u6574\u6570\u636e\u4fdd\u6301\u4e00\u81f4\uff09\u3002<\/p>\n

## \u5c0f\u9f20 ESC \u6570\u636e\u5b50\u96c6<\/p>\n

data(“example_sce”, package = “scMerge”)<\/p>\n

data(“segList_ensemblGeneID”, package = “scMerge”)<\/p>\n

\u5728\u8fd9\u4e2a mESC \u6570\u636e\u4e2d\uff0c\u6211\u4eec\u6c47\u96c6\u4e86\u6765\u81ea\u4e09\u79cd\u4e0d\u540c\u7ec6\u80de\u7c7b\u578b\u7684\u4e24\u4e2a\u4e0d\u540c\u6279\u6b21\u7684\u6570\u636e\u3002\u901a\u8fc7 PCA \u56fe\uff0c\u6211\u4eec\u53ef\u4ee5\u770b\u5230\uff0c\u5c3d\u7ba1\u7ec6\u80de\u7c7b\u578b\u6709\u5f88\u5f3a\u7684\u5206\u79bb\u6027\uff0c\u4f46\u6279\u6b21\u6548\u5e94\u4e5f\u9020\u6210\u4e86\u5f88\u5f3a\u7684\u5206\u79bb\u6027\u3002<\/p>\n

example_sce = runPCA(example_sce, exprs_values = “logcounts”)<\/p>\n

scater::plotPCA(example_sce,<\/p>\n

colour_by = “cellTypes”,<\/p>\n

shape_by = “batch”)<\/p>\n

<\/p>\n

\u65e0\u76d1\u7763 scMerge2<\/strong><\/p>\n

\u5728\u65e0\u76d1\u7763\u60c5\u51b5\u4e0b\uff0c\u6211\u4eec\u5c06\u5bf9\u6bcf\u4e2a\u6279\u6b21\u4e2d\u7684\u5171\u4eab\u8fd1\u90bb\u56fe\u8fdb\u884c\u56fe\u805a\u7c7b\uff0c\u4ee5\u83b7\u5f97\u4f2a\u526f\u672c\u3002\u8fd9\u9700\u8981\u7528\u6237\u63d0\u4f9b\u4e00\u4e2a\u5411\u91cf\uff0c\u5176\u4e2d\u5305\u542b\u6bcf\u4e2a\u6279\u6b21\u4e2d\u6784\u5efa\u6700\u8fd1\u90bb\u56fe\u65f6\u7684\u90bb\u56fe\u6570\u91cf\u3002\u9ed8\u8ba4\u60c5\u51b5\u4e0b\u4e3a10\u3002<\/p>\n

scMerge2_res <- scMerge2(exprsMat = logcounts(example_sce),<\/p>\n

batch = example_sce$batch,<\/p>\n

ctl = segList_ensemblGeneID$mouse$mouse_scSEG,<\/p>\n

verbose = FALSE)<\/p>\n

assay(example_sce, “scMerge2”) <- scMerge2_res$newY<\/p>\n

set.seed(2022)<\/p>\n

example_sce <- scater::runPCA(example_sce, exprs_values = ‘scMerge2’)<\/p>\n

scater::plotPCA(example_sce, colour_by = ‘cellTypes’, shape = ‘batch’)<\/p>\n

<\/p>\n

\u534a\u76d1\u7763scMerge2<\/strong><\/p>\n

scMerge2_res <- scMerge2(exprsMat = logcounts(example_sce),<\/p>\n

batch = example_sce$batch,<\/p>\n

cellTypes = example_sce$cellTypes,<\/p>\n

ctl = segList_ensemblGeneID$mouse$mouse_scSEG,<\/p>\n

verbose = FALSE)<\/p>\n

assay(example_sce, “scMerge2”) <- scMerge2_res$newY<\/p>\n

example_sce = scater::runPCA(example_sce, exprs_values = ‘scMerge2’)<\/p>\n

scater::plotPCA(example_sce, colour_by = ‘cellTypes’, shape = ‘batch’)<\/p>\n

<\/p>\n

scMerge2 \u7684\u66f4\u591a\u8be6\u7ec6\u4fe1\u606f<\/strong><\/p>\n

\u6bcf\u4e2a\u5355\u5143\u683c\u5206\u7ec4\u5185\u6784\u5efa\u7684\u4f2a\u5757\u6570\u91cf\u9ed8\u8ba4\u8bbe\u7f6e\u4e3a 30\u3002\u6570\u5b57\u8d8a\u5927\uff0c\u6a21\u578b\u4f30\u7b97\u4e2d\u7684\u4f2a\u5757\u6570\u636e\u5c31\u8d8a\u591a\uff0c\u4f30\u7b97\u65f6\u95f4\u4e5f\u5c31\u8d8a\u957f\u3002<\/p>\n

scMerge2_res <- scMerge2(exprsMat = logcounts(example_sce),<\/p>\n

batch = example_sce$batch,<\/p>\n

ctl = segList_ensemblGeneID$mouse$mouse_scSEG,<\/p>\n

k_pseudoBulk = 50,<\/p>\n

verbose = FALSE)<\/p>\n

assay(example_sce, “scMerge2”) <- scMerge2_res$newY<\/p>\n

set.seed(2022)<\/p>\n

example_sce <- scater::runPCA(example_sce, exprs_values = ‘scMerge2’)<\/p>\n

scater::plotPCA(example_sce, colour_by = ‘cellTypes’, shape = ‘batch’)<\/p>\n

<\/p>\n

\u5728\u5904\u7406\u5927\u91cf\u6570\u636e\u65f6\uff0c\u6211\u4eec\u53ef\u4ee5\u6bcf\u6b21\u83b7\u53d6\u8f83\u5c0f\u5355\u5143\u683c\u5b50\u96c6\u7684\u8c03\u6574\u540e\u77e9\u9635\u3002\u8fd9\u53ef\u4ee5\u901a\u8fc7\u5728in\u51fd\u6570\u4e2d\u8bbe\u7f6e\uff0c\u51fd\u6570\u5c06\u4e0d\u8fd4\u56de\u8c03\u6574\u540e\u7684\u6574\u4e2a\u77e9\u9635\uff0c\u800c\u662f\u8f93\u51fa\u4f30\u8ba1\u503c\u3002\u7136\u540e\uff0c\u4e3a\u4e86\u4f7f\u7528\u4f30\u8ba1\u503c\u5f97\u5230\u8c03\u6574\u540e\u7684\u77e9\u9635\uff0c\u6211\u4eec\u9996\u5148\u9700\u8981\u5bf9\u5bf9\u6570\u77e9\u9635\u8fdb\u884c\u4f59\u5f26\u5f52\u4e00\u5316\u5904\u7406\uff0c\u7136\u540e\u8ba1\u7b97\u4f59\u5f26\u5f52\u4e00\u5316\u77e9\u9635\u7684\u884c\u5411\uff08\u57fa\u56e0\u5411\uff09\u5e73\u5747\u503c\uff08\u8fd9\u662f\u56e0\u4e3a\u9ed8\u8ba4\u60c5\u51b5\u4e0b\uff0c\u5728\u6b65\u9aa4\u4e4b\u524d\u4f1a\u5bf9\u5bf9\u6570\u5f52\u4e00\u5316\u77e9\u9635\u8fdb\u884c\u4f59\u5f26\u5f52\u4e00\u5316\u5904\u7406\uff09\u3002\u7136\u540e\uff0c\u6bcf\u6b21\u6211\u4eec\u90fd\u53ef\u4ee5\u7528\u5b83\u6765\u8c03\u6574\u5355\u5143\u683c\u5b50\u96c6\u7684\u77e9\u9635\u3002<\/p>\n

scMerge2_res <- scMerge2(exprsMat = logcounts(example_sce),<\/p>\n

batch = example_sce$batch,<\/p>\n

ctl = segList_ensemblGeneID$mouse$mouse_scSEG,<\/p>\n

verbose = FALSE,<\/p>\n

return_matrix = FALSE)<\/p>\n

cosineNorm_mat <- batchelor::cosineNorm(logcounts(example_sce))<\/p>\n

adjusted_means <- DelayedMatrixStats::rowMeans2(cosineNorm_mat)<\/p>\n

newY <- list()<\/p>\n

for (i in levels(example_sce$batch)) {<\/p>\n

newY[[i]] <- getAdjustedMat(cosineNorm_mat[, example_sce$batch == i],<\/p>\n

scMerge2_res$fullalpha,<\/p>\n

ctl = segList_ensemblGeneID$mouse$mouse_scSEG,<\/p>\n

ruvK = 20,<\/p>\n

adjusted_means = adjusted_means)<\/p>\n

}<\/p>\n

newY <- do.call(cbind, newY)<\/p>\n

assay(example_sce, “scMerge2”) <- newY[, colnames(example_sce)]<\/p>\n

set.seed(2022)<\/p>\n

example_sce <- scater::runPCA(example_sce, exprs_values = ‘scMerge2’)<\/p>\n

scater::plotPCA(example_sce, colour_by = ‘cellTypes’, shape = ‘batch’)<\/p>\n

<\/p>\n

scMerge2 \u4e3a\u9700\u8981\u901a\u8fc7\u51fd\u6570\u8fdb\u884c\u591a\u7ea7\u8c03\u6574\u7684\u6570\u636e\u6574\u5408\u63d0\u4f9b\u4e86\u5206\u7ea7\u5408\u5e76\u7b56\u7565\u3002\u4f8b\u5982\uff0c\u5bf9\u4e8e\u6709\u591a\u4e2a\u6837\u672c\u7684\u6570\u636e\u96c6\uff0c\u6211\u4eec\u53ef\u80fd\u5e0c\u671b\u5148\u6d88\u9664\u6570\u636e\u96c6\u5185\u90e8\u7684\u6837\u672c\u6548\u5e94\uff0c\u7136\u540e\u518d\u4e0e\u5176\u4ed6\u6570\u636e\u96c6\u6574\u5408\u3002\u4e0b\u9762\uff0c\u6211\u4eec\u5c06\u8bf4\u660e\u5982\u4f55\u5efa\u7acb\u5206\u5c42\u5408\u5e76\u987a\u5e8f\uff0c\u4f5c\u4e3ascMerge2h()scMerge2h() \u7684\u8f93\u5165\u3002<\/p>\n

\u4e3a\u4e86\u4fbf\u4e8e\u8bf4\u660e\uff0c\u6211\u9996\u5148\u4e3a\u6837\u672c\u6570\u636e\u521b\u5efa\u4e86\u4e00\u4e2a\u5047\u6837\u672c\u4fe1\u606f\u3002\u73b0\u5728\uff0c\u6bcf\u4e2a\u6279\u6b21\u90fd\u6709\u4e24\u4e2a\u6837\u672c\u3002<\/p>\n

# \u521b\u5efa\u4e00\u4e2a\u5047\u6837\u672c\u4fe1\u606f<\/p>\n

example_sce$sample <- rep(c(1:4), each = 50)<\/p>\n

table(example_sce$sample, example_sce$batch)<\/p>\n

\u8981\u6267\u884c\u5408\u5e76\uff0c\u6211\u4eec\u9700\u8981\u521b\u5efa\u4e00\u4e2a\u5206\u5c42\u7d22\u5f15\u5217\u8868scMerge2h<\/p>\n

1.\u4e00\u4e2a\u5206\u5c42\u7d22\u5f15\u5217\u8868\uff0c\u8868\u793a\u8981\u5408\u5e76\u7684\u5355\u5143\u683c\u7684\u7d22\u5f15\uff1b<\/p>\n

2.\u4e00\u4e2a\u6279\u6b21\u4fe1\u606f\u5217\u8868\uff0c\u8868\u793a\u6bcf\u6b21\u5408\u5e76\u7684\u6279\u6b21\u4fe1\u606f\u3002<\/p>\n

\u573a\u666f1<\/strong><\/p>\n

\u6211\u4eec\u5c06\u9996\u5148\u8bf4\u660e\u4e24\u7ea7\u5408\u5e76\u7684\u60c5\u51b5\uff0c\u5176\u4e2d\u7b2c\u4e00\u7ea7\u662f\u6307\u5728\u6bcf\u4e00\u6279\u4e2d\u53bb\u9664\u6837\u672c\u6548\u5e94\uff0c\u7b2c\u4e8c\u7ea7\u662f\u6307\u4e24\u6279\u7684\u5408\u5e76\u3002<\/p>\n

\u9996\u5148\uff0c\u6211\u4eec\u5c06\u6784\u5efa\u5206\u5c42\u7d22\u5f15\u5217\u8868\u3002\u5206\u5c42\u7d22\u5f15\u5217\u8868\u662f\u4e00\u4e2a\u5217\u8868\uff0c\u5b83\u6307\u51fa\u4e86\u6bcf\u4e00\u5c42\u4e2d\u54ea\u4e9b\u5355\u5143\u683c\u7684\u7d22\u5f15\u8981\u8fdb\u884c\u5408\u5e76\u3002\u5217\u8868\u5143\u7d20\u7684\u6570\u91cf\u5e94\u4e0e\u5408\u5e76\u5c42\u7ea7\u7684\u6570\u91cf\u76f8\u540c\u3002\u5bf9\u4e8e\u6bcf\u4e2a\u5143\u7d20\uff0c\u5b83\u5e94\u5305\u542b\u6bcf\u4e2a\u5408\u5e76\u5355\u5143\u7684\u7d22\u5f15\u5411\u91cf\u5217\u8868\u3002<\/p>\n

# \u6784\u5efa\u5206\u5c42\u7d22\u5f15\u5217\u8868<\/p>\n

h_idx_list <- list(level1 = split(seq_len(ncol(example_sce)), example_sce$batch),<\/p>\n

level2 = list(seq_len(ncol(example_sce))))<\/p>\n

\u5728\u7b2c 1 \u5c42\uff0c\u6211\u4eec\u5c06\u6267\u884c\u4e24\u6b21\u5408\u5e76\uff0c\u6bcf\u4e00\u6279\u5408\u5e76\u4e00\u6b21\u3002\u56e0\u6b64\uff0c\u6211\u4eec\u6709\u4e00\u4e2a\u7531\u4e24\u4e2a\u7d22\u5f15\u5411\u91cf\u7ec4\u6210\u7684\u5217\u8868\u3002\u6bcf\u4e2a\u77e2\u91cf\u8868\u793a\u5404\u6279\u6b21\u5355\u5143\u683c\u7684\u7d22\u5f15\u3002<\/p>\n

h_idx_list$level1<\/p>\n

<\/p>\n

\u5728\u7b2c 2 \u5c42\uff0c\u6211\u4eec\u5c06\u6267\u884c\u4e00\u6b21\u5408\u5e76\uff0c\u5408\u5e76\u4e24\u6279\u6570\u636e\u3002\u56e0\u6b64\uff0c\u6211\u4eec\u6709\u4e00\u4e2a\u7d22\u5f15\u5411\u91cf\u5217\u8868\uff0c\u8868\u793a\u5b8c\u6574\u6570\u636e\u4e2d\u6240\u6709\u5355\u5143\u683c\u7684\u7d22\u5f15\u3002<\/p>\n

h_idx_list$level2<\/p>\n

<\/p>\n

\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u9700\u8981\u521b\u5efa\u6279\u6b21\u4fe1\u606f\u5217\u8868\u3002<\/p>\n

# \u6784\u5efa\u6279\u6b21\u4fe1\u606f\u5217\u8868<\/p>\n

batch_list <- list(level1 = split(example_sce$sample, example_sce$batch),<\/p>\n

level2 = list(example_sce$batch))<\/p>\n

\u6211\u4eec\u53ef\u4ee5\u770b\u5230\u6807\u6709\u5408\u5e76\u7ea7\u522b\u7684batch_list\u3002<\/p>\n

batch_list$level1<\/p>\n

<\/p>\n

\u73b0\u5728\uff0c\u6211\u4eec\u53ef\u4ee5\u8f93\u5165and\u6765\u5206\u5c42\u5408\u5e76\u6570\u636e\u3002\u6211\u4eec\u8fd8\u9700\u8981\u8f93\u5165 a \uff0c\u5b83\u662f\u6bcf\u4e2a\u5408\u5e76\u5c42\u7ea7\u7684\u65e0\u7528\u53d8\u5f02\u6570\uff08RUV \u6a21\u578b\u4e2d\u4e3a k\uff09\u7684\u5411\u91cf\u3002\u6211\u4eec\u5efa\u8bae\u5728\u7b2c\u4e00\u5c42\u8f93\u5165\u8f83\u4f4e\u7684\u3002\u5728\u8fd9\u91cc\uff0c\u6211\u4eec\u5c06 RUV \u7684 k \u8bbe\u7f6e\u4e3a\u7b2c\u4e00\u5c42\u4e3a 2\uff0c\u7b2c\u4e8c\u5c42\u4e3a 5\u3002batch_listh_idx_listscMerge2hruvK_listruvKruvK_list = c(2, 5)<\/p>\n

scMerge2_res <- scMerge2h(exprsMat = logcounts(example_sce),<\/p>\n

batch_list = batch_list,<\/p>\n

h_idx_list = h_idx_list,<\/p>\n

ctl = segList_ensemblGeneID$mouse$mouse_scSEG,<\/p>\n

ruvK_list = c(2, 5),<\/p>\n

verbose = FALSE)<\/p>\n

scMerge2h \u7684\u8f93\u51fa\u662f\u4e00\u4e2a\u77e9\u9635\u5217\u8868\uff0c\u663e\u793a\u6bcf\u4e00\u7ea7\u8c03\u6574\u540e\u7684\u77e9\u9635\u3002<\/p>\n

length(scMerge2_res)<\/p>\n

lapply(scMerge2_res, dim)<\/p>\n

\u5728\u6b64\uff0c\u6211\u4eec\u5c06\u4f7f\u7528\u4e0a\u4e00\u7ea7\u7684\u8c03\u6574\u77e9\u9635\u4f5c\u4e3a\u6700\u7ec8\u8c03\u6574\u77e9\u9635\u3002<\/p>\n

assay(example_sce, “scMerge2”) <- scMerge2_res[[length(h_idx_list)]]<\/p>\n

set.seed(2022)<\/p>\n

example_sce <- scater::runPCA(example_sce, exprs_values = ‘scMerge2’)<\/p>\n

scater::plotPCA(example_sce, colour_by = ‘cellTypes’, shape = ‘batch’)<\/p>\n

<\/p>\n

\u573a\u666f2<\/strong><\/p>\n

scMerge2h \u53ef\u4ee5\u5904\u7406\u7075\u6d3b\u7684\u5408\u5e76\u7b56\u7565\u8f93\u5165\u3002\u4f8b\u5982\uff0c\u5728\u4e0a\u8ff0\u7b2c 1 \u5c42\uff0c\u6211\u4eec\u53ea\u80fd\u5408\u5e76\u4e00\u4e2a\u6279\u6b21\u7684\u6570\u636e\u3002\u4f8b\u5982\uff0c\u6211\u4eec\u53ef\u4ee5\u4ece\u4fee\u6539\u6279\u6b21\u7d22\u5f15\u5217\u8868\u548c\u5206\u5c42\u7d22\u5f15\u5217\u8868\u5f00\u59cb\uff0c\u5220\u9664\u7b2c 1 \u5c42\u7684\u7b2c 2 \u6279\u5217\u8868\u3002<\/p>\n

h_idx_list2 <- h_idx_list<\/p>\n

batch_list2 <- batch_list<\/p>\n

h_idx_list2$level1$batch2 <- NULL<\/p>\n

batch_list2$level1$batch2 <- NULL<\/p>\n

print(h_idx_list2)<\/p>\n

<\/p>\n

print(batch_list2)<\/p>\n

<\/p>\n

scMerge2_res <- scMerge2h(exprsMat = logcounts(example_sce),<\/p>\n

batch_list = batch_list2,<\/p>\n

h_idx_list = h_idx_list2,<\/p>\n

ctl = segList_ensemblGeneID$mouse$mouse_scSEG,<\/p>\n

ruvK_list = c(2, 5),<\/p>\n

verbose = FALSE)<\/p>\n

assay(example_sce, “scMerge2”) <- scMerge2_res[[length(h_idx_list)]]<\/p>\n

set.seed(2022)<\/p>\n

example_sce <- scater::runPCA(example_sce, exprs_values = ‘scMerge2’)<\/p>\n

scater::plotPCA(example_sce, colour_by = ‘cellTypes’, shape = ‘batch’)<\/p>\n

<\/p>\n

\u7ed3\u8bed<\/strong><\/p>\n

scMerge2\u80fd\u591f\u5bf9\u5927\u91cf\u5355\u7ec6\u80de\u6570\u636e\u8fdb\u884c\u7efc\u5408\u5206\u6790\u3002\u968f\u7740\u516c\u5171\u591a\u6837\u672c\u591a\u6761\u4ef6\u5355\u7ec6\u80de\u7814\u7a76\u7684\u53ef\u7528\u6027\u6301\u7eed\u6fc0\u589e\uff0cscMerge2 \u8bc1\u660e\u4e86\u5176\u6574\u5408\u8d85\u8fc7 500 \u4e07\u4e2a\u7ec6\u80de\u4ee5\u8fdb\u884c\u8fdb\u4e00\u6b65\u4e0b\u6e38\u5206\u6790\u7684\u80fd\u529b\uff0c\u4ece\u800c\u5b9e\u73b0\u6709\u6548\u7684\u4e0b\u6e38\u835f\u8403\u5206\u6790\u3002scMerge2\u5728\u6240\u6709\u4e3b\u8981\u7ec6\u80de\u7c7b\u578b\u7684\u9884\u6d4b\u51c6\u786e\u7387\u65b9\u9762\u6709\u4e86\u663e\u7740\u7684\u63d0\u9ad8\u3002\u6700\u540e\uff0cscMerge2\u80fd\u591f\u7ed3\u5408\u4ece\u5404\u79cd\u5355\u7ec6\u80de\u6280\u672f\uff08\u5982CITE-seq\uff0cCyTOF\u548c\u56fe\u50cf\u8d28\u8c31\u7ec6\u80de\u672f\uff09\u83b7\u5f97\u7684\u6570\u767e\u4e07\u4e2a\u7ec6\u80de\u7684\u6570\u636e\u3002<\/p>\n

\u597d\u4e86\uff0c\u5c0f\u679c\u5e26\u7740\u5927\u5bb6\u5df2\u7ecf\u5b66\u4e60\u4e8680%\u7684\u77e5\u8bc6\u4e86\uff0c\u5269\u4e0b\u7684\u5185\u5bb9\u5c31\u4ea4\u7ed9\u5c0f\u4f19\u4f34\u4eec\u4e86\uff01\u6700\u540e\uff0c\u5927\u5bb6\u5982\u679c\u5bf9\u5355\u7ec6\u80de\u6570\u636e\u5206\u6790\u8fd8\u4e0d\u719f\u6089\uff0c\u53c8\u60f3\u5c1d\u8bd5\u4e00\u4e0b\u5904\u7406\u81ea\u5df1\u7684\u6570\u636e\uff0c\u4e0d\u59a8\u8bd5\u4e00\u4e0b\u5c0f\u679c\u5f00\u53d1\u7684\u751f\u4fe1\u4e91\u5e73\u53f0\u54e6\uff0c\u4e00\u952e\u51fa\u56fe\uff0c\u4e00\u952e\u5bfc\u51faCNS\u7ea7\u522b\u7684Figture\uff01\uff01\u8d76\u5feb\u53bb\u8bd5\u8bd5\u5427\uff01\uff01\u70b9\u51fb http:\/\/www.biocloudservice.com\/home.html\u3002<\/p>\n

\u53c2\u8003\u6587\u732e<\/strong><\/p>\n

    \n
  1. scMerge: scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets. Yingxin Lin, Shila Ghazanfar, Kevin Y.X. Wang, Johann A. Gagnon-Bartsch, Kitty K. Lo, Xianbin Su, Ze-Guang Han, John T. Ormerod, Terence P. Speed, Pengyi Yang, Jean Y. H. Yang. (2019). Our manuscript published at PNAS can be found here.<\/li>\n
  2. scMerge2: Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2. Yingxin Lin, Yue Cao, Elijah Willie, Ellis Patrick, Jean Y.H. Yang. (2023). Our manuscript published in Nature Communications can be found here.<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

    \u524d\u8a00 \u5355\u7ec6\u80de\u591a\u6837\u672c\u6574\u5408\u5de5\u5177\u5927\u5bb6\u4e5f\u5b66\u8fc7\u5f88\u591a\u4e86\u5427\uff01\u4f46\u662f\u9664\u4e86 Seurat\u3001SAUCIE \u548c Scanorama \u4e4b […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/27751"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=27751"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/27751\/revisions"}],"predecessor-version":[{"id":27768,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/27751\/revisions\/27768"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=27751"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=27751"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=27751"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}