单细胞测序从rds转loom

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已于 2024-03-05 14:30:16 修改

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文章标签： java 前端服务器

于 2023-10-20 15:36:32 首次发布

本文链接：https://blog.csdn.net/qq_45978569/article/details/133947851

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#先设置好路径
getwd()
setwd("E:/scRNA data/")
library("Seurat")
library("sceasy")
library("loomR")
#导入seurat文件
fi <- readRDS('E:/scRNA data/filename.rds') 
#从seurat转化为sce
pfile1 <-sceasy::convertFormat(fi, from="seurat", to="sce",outFile='sce.rds')
#从sce转化为loom
fi <- readRDS('E:/scRNA data/sce.rds')
pfile1 <-sceasy::convertFormat(fi, from="sce", to="loom", outFile='loom.loom')

备用

# 备用
# Seurat 转 AnnData
# sceasy::convertFormat(seurat_object, from="seurat", to="anndata",outFile='filename.h5ad')
# 
# AnnData 转 Seurat
# sceasy::convertFormat(h5ad_file, from="anndata", to="seurat",outFile='filename.rds')
# 
# Seurat 转 SingleCellExperiment
# sceasy::convertFormat(seurat_object, from="seurat", to="sce", outFile='filename.rds')
# 
# SingleCellExperiment 转 AnnData
# sceasy::convertFormat(sce_object, from="sce", to="anndata",outFile='filename.h5ad')
# 
# SingleCellExperiment 转 Loom
# sceasy::convertFormat(sce_object, from="sce", to="loom",outFile='filename.loom')
# 
# Loom 转 AnnData
# sceasy::convertFormat('filename.loom', from="loom", to="anndata",outFile='filename.h5ad')
# 
# Loom 转SingleCellExperiment
# sceasy::convertFormat('filename.loom', from="loom", to="sce",outFile='filename.rds')
#