使用函数seurat::merge()整合两个或多个数据集。 Seurat V4: 示例1:合并两个10X PBMC数据集: 首先读入并创建两个seurat objects: pbmc4k和pbmc8k rm(list=ls()) options(stringsAsFactors = F) setwd("D:/bioinformatics/scRNA-seq/0. background/data")
#4我们有两个seuratv5的对象,进行整合分析---merged_obj<-merge(x=ifnb_list$CTRL,y=ifnb_list$STIM)merged_obj<-NormalizeData(merged_obj)merged_obj<-FindVariableFeatures(merged_obj)merged_obj<-ScaleData(merged_obj)merged_obj<-RunPCA(merged_obj)obj=merged_obj#rpcaobj<-Integrate...
# Merge two Seurat objects merge(x = pbmc1, y = pbmc2) # Merge more than two Seurat objects merge(x = pbmc1, y = list(pbmc2, pbmc3)) 数据访问 在Seurat 中访问数据很简单,使用明确定义的取子集代码可以快速查找所需的数据。 代码语言:javascript 代码运行次数:0 运行 AI代码解释 # View me...
# add information to identify dataset of origin pbmc500$dataset <- 'pbmc500' pbmc1k$dataset <- 'pbmc1k' pbmc5k$dataset <- 'pbmc5k' pbmc10k$dataset <- 'pbmc10k' # merge all datasets, adding a cell ID to make sure cell names are unique combined <- merge( x = pbmc500, y = list(...
# merge all datasets, adding a cell ID to make sure cell names are unique combined <- merge( x = pbmc500, y = list(pbmc1k, pbmc5k, pbmc10k), add.cell.ids = c("500", "1k", "5k", "10k") ) combined[["ATAC"]] ## ChromatinAssay data with 89951 features for 21688 cells ...
# Downsample the number of cells per identity classsubset(x = pbmc, downsample = 100)# Merge two Seurat objectsmerge(x = pbmc1, y = pbmc2)# Merge more than two Seurat objectsmerge(x = pbmc1, y = list(pbmc2, pbmc3)) 数据访问 在Seurat 中访问数据很简单,使用明确定义的取子集代码可以...
# add information to identify dataset of originpbmc500$dataset<-'pbmc500'pbmc1k$dataset<-'pbmc1k'pbmc5k$dataset<-'pbmc5k'pbmc10k$dataset<-'pbmc10k'# merge all datasets, adding a cell ID to make sure cell names are uniquecombined<-merge(x=pbmc500,y=list(pbmc1k,pbmc5k,pbmc10k),add.cell...
Sorry for our slow response on this. Can you please post the full code you're using to merge v5 objects in a for loop? Thanks! @mhkowalski Hi, It seems I'm having a similar issue, when merging different sample of the same dataset into one seurat object using a loop, the layers' ...
In CheckDuplicateCellNames(object.list = objects) : Some cell names are duplicated across objects provided. Renaming to enforce unique cell names.' Fyi: the merge worked with a smaller cell number with this dataset, but with other dataset it did work for whatever size. ...
list()# 作者没有保留其计算过程 DimPlot(object = reference, reduction ="wnn.umap", group.by ="celltype.l2", label = TRUE, label.size = 3, repel = TRUE) + NoLegend() 为了演示到这个多模态参考的映射,我们将使用由10x Genomics产生的2700个PBMCs的数据集,并通过SeuratData包调取。