seurat_data <- newimport(SeuratObject) ###重新定义了import函数,称为newimport newimport <- function(otherCDS, import_all = FALSE) { if(class(otherCDS)[1] == 'Seurat') { requireNamespace("Seurat") data <- otherCDS@assays$RNA@counts if(class(data) == "data.frame") { data <- as...
We next use the count matrix to create aSeuratobject. The object serves as a container that contains both data (like the count matrix) and analysis (like PCA, or clustering results) for a single-cell dataset. For a technical discussion of theSeuratobject structure, check out ourGitHub Wiki....
seurat_data<-newimport(SeuratObject)###重新定义了import函数,称为newimport newimport<-function(otherCDS,import_all=FALSE){if(class(otherCDS)[1]=='Seurat'){requireNamespace("Seurat")data<-otherCDS@assays$RNA@countsif(class(data)=="data.frame"){data<-as(as.matrix(data),"sparseMatrix")}pd...
一、读入数据。 Read10X()和CreateSeuratObject()函数就是根据输入矩阵/数据框,创建Seurat对象的。重要步骤是 设置 ident 和添加 meta.data。 dat <- Read10X(data.dir = "your/work/path") organoids <- CreateSeuratObject(counts = dat, project = "Organoids", min.cells = 3, min.features = 200) ...
其实Seurat 团队考虑到了这一点,在3中提供了由2 到3转化的函数:-UpdateSeuratObject: FAQ >library(Seurat)# 我是V3>mm<-readRDS("Seurat.old/mmm.rds")>mm An old seurat object19600genes across11700samples>newMM<-UpdateSeuratObject(mm)Validating object structure ...
./seurat-4.1.0/R/visualization.R:3667:ElbowPlot <- function(object, ndims = 20, reduction = 'pca') { 选择相关的维度,这个比 Jackstraw 要快得多。 #' Quickly Pick Relevant Dimensions #' #' Plots the standard deviations (or approximate singular values if running PCAFast) #' of the princip...
seurat_data <- newimport(SeuratObject) ###重新定义了import函数,称为newimport newimport <- function(otherCDS, import_all = FALSE) { if(class(otherCDS)[1] == 'Seurat') { requireNamespace("Seurat") data <- otherCDS@assays$RNA@counts ...
error in as.data.frame.default(x[[i]], optional = true) : cannot coerce class ‘structure("seurat", package = "seuratobject")’ to a data.frame 文心快码BaiduComate 针对你提出的问题,我将分点进行回答,并提供相应的代码片段作为佐证。 理解错误信息: 错误信息表明,as.data.frame.default函数在...
To maintain compatibility with previous workflows, new Seurat objects will use the previous object structure by default To use new Seurat v5 assays: Please run: options(Seurat.object.assay.version = 'v5') packageVersion('Seurat') [1] ‘4.9.9.9050’ ...
An object of class Seurat 142514 features across 11909 samples within 2 assays Active assay: RNA (36601 features, 0 variable features) 1 other assay present: ATAC 我们根据每种模式检测到的分子数以及线粒体百分比来执行基本的QC,其实这一步什么也没有Q掉,只是获得数据概览,了解数据的质量分布。