应用单细胞测序技术对左侧和右侧结直肠癌进行特征分析

GSM5688706 Left-sided CRC 1
GSM5688707 Left-sided CRC 2
GSM5688708 Left-sided CRC 3
GSM5688709 Right-sided CRC 1
GSM5688710 Right-sided CRC 2
GSM5688711 Right-sided CRC 3

GSM5688706_barcodes_WGC.tsv.gz 23.3 Kb
GSM5688706_features_WGC.tsv.gz 274.6 Kb
GSM5688706_matrix_WGC.mtx.gz 20.3 Mb
GSM5688707_barcodes_JCA.tsv.gz 22.2 Kb
GSM5688707_features_JCA.tsv.gz 274.6 Kb
GSM5688707_matrix_JCA.mtx.gz 25.8 Mb
GSM5688708_barcodes_LS-CRC3.tsv.gz 29.6 Kb
GSM5688708_features_LS-CRC3.tsv.gz 274.6 Kb
GSM5688708_matrix_LS-CRC3.mtx.gz 27.8 Mb
GSM5688709_barcodes_RS-CRC1.tsv.gz 28.4 Kb
GSM5688709_features_RS-CRC1.tsv.gz 274.6 Kb
GSM5688709_matrix_RS-CRC1.mtx.gz 28.0 Mb
GSM5688710_barcodes_R_CRC3.tsv.gz 21.0 Kb
GSM5688710_features_R_CRC3.tsv.gz 274.6 Kb
GSM5688710_matrix_R_CRC3.mtx.gz 17.3 Mb
GSM5688711_barcodes_R_CRC4.tsv.gz 30.0 Kb
GSM5688711_features_R_CRC4.tsv.gz 274.6 Kb
GSM5688711_matrix_R_CRC4.mtx.gz 27.3 Mb

###### step1:导入数据 ######  

library(data.table)
dir='GSE188711_RAW/outputs/' 
samples=list.files( dir )
samples 

library(data.table)
sceList = lapply(samples,function(pro){ 
  # pro=samples[1] 
  print(pro) 
  sce=CreateSeuratObject( Read10X(file.path(dir,pro)), 
                          project = pro,
                         min.cells = 5,
                         min.features = 300 ) 
  return(sce)
})
names(sceList)  
 
samples
sce.all=merge(x=sceList[[1]],
              y=sceList[ -1 ],
              add.cell.ids = samples)

as.data.frame(sce.all@assays$RNA@counts[1:10, 1:2])
head(sce.all@meta.data, 10)
table(sce.all$orig.ident)