3
Single-Cell Transcriptomic Analysis of Human Lung Provides Insights
into the Pathobiology of Pulmonary Fibrosis

_使用seurat sct方法中的reference based處理大數(shù)據(jù)超過100000個細胞

library(Seurat) library(hdf5r) library(dplyr)getwd()path="G:/silicosis/geo/GSE122960_ScRNA_ of Human Lung During Pulmonary Fibrosis II/GSE122960_RAW/filter_.h5/" setwd(path)# H5文件讀入和轉(zhuǎn)化為Seurat對象 # https://nbisweden.github.io/workshop-scRNAseq/labs/compiled/seurat/seurat_01_qc.htmlfs=list.files(pattern = '.h5') fs sceList = lapply(fs, function(x){# x=fs[1]print(x)a=Read10X_h5( x )a[1:4,1:4] library(stringr)(p=str_split(x,'_',simplify = T)[,2])sce <- CreateSeuratObject( a ,project = p )sce }) setwd('../') getwd()names(sceList) length(sceList) sceList[[1]]for (i in 1:length(sceList) ) {sceList[[i]]=SCTransform(sceList[[i]],verbose = FALSE) }sceList.features=SelectIntegrationFeatures(object.list = sceList,nfeatures = 3000) sceList=PrepSCTIntegration(object.list = sceList,anchor.features = sceList.features)reference_dataset=c(sceList[[14]],sceList[[15]])sceList.anchors=FindIntegrationAnchors(object.list = sceList,

anchor.features = sceList.features,reference = reference_dataset) sceList.integrated=IntegrateData(anchorset = sceList.anchors,normalization.method = "SCT") sceList.integrated=sceList.integrated %>%RunPCA(verbose=FALSE) %>%RunUMAP(dims=1:30)

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