# #——包括= FALSE --------------------------------------------------------- knitr: opts_chunk美元集(崩溃= TRUE,发表评论 = "#>" ) ## ---- eval = FALSE ------------------------------------------------------------ # 库(遥控器)#遥控器::install_github(“ilia-kats / MuData ") ## ---- 设置中,消息= FALSE --------------------------------------------------- 库(MuData)库(SingleCellExperiment)图书馆(MultiAssayExperiment)图书馆(SingleCellMultiModal)图书馆(嘘)图书馆(rhdf5 ) ## ----------------------------------------------------------------------------- 美< - CITEseq(数据类型=“cord_blood”,模式=“*”,dry.run = FALSE,version = " 1.0.0 ")美 ## ----------------------------------------------------------------------------- # 定义转换CLR在修工作流CLR < - t(数据)函数(应用(数据、1、函数(x) log1p (x / (exp(总和(log1p (x (x > 0)) na。rm /长度(x = TRUE) ))) )) ) ## ----------------------------------------------------------------------------- adt_counts < -美[[“scADT”]]美[[“scADT”]]< - SingleCellExperiment (adt_counts)试验(mae[[“scADT”]],clr) < - clr (adt_counts ) ## ----------------------------------------------------------------------------- 美[[" scADT "]] < runPCA (mae[[“scADT”]],exprs_values =“clr”,ncomponents = 20 ) ## ----------------------------------------------------------------------------- plotReducedDim (mae [[" scADT "]], dimred =“PCA by_exprs_values =“clr colour_by = CD3) plotReducedDim (mae[[“scADT”]],dimred =“PCA by_exprs_values =“clr colour_by = " CD14 ") ## ----------------------------------------------------------------------------- writeH5MU(美“cord_blood_citeseq.h5mu ") ## ----------------------------------------------------------------------------- h5 < - rhdf5: H5Fopen(“cord_blood_citeseq.h5mu”)h5ls (H5Gopen (h5,“国防部”),递归= FALSE ) ## ----------------------------------------------------------------------------- h5ls (H5Gopen (h5、“国防部/ scADT”),递归= FALSE) h5ls (H5Gopen (h5,“国防部/ scADT /层”),递归= FALSE ) ## ----------------------------------------------------------------------------- h5ls (H5Gopen (h5,“国防部/ scADT / obsm”),递归= FALSE) #有另一种方法来访问组:# h5“国防部”&“scADT”&“obsm”rhdf5:: H5close () ## ----------------------------------------------------------------------------- sessionInfo ()