2020-07-07 单细胞数据.h5文件转换成seurat对象

第一步：从GEO数据库下载.h5文件

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3892578

第二步:Rstudio加载包，读入数据

        library(Seurat)

        library(ggplot2)

        library(cowplot)

        library(Matrix)

        library(dplyr)

        library(ggsci)

        library(scater)

        library(SingleR)

        library(hdf5r)

###用read10x_h5函数读取数据

        Read10X_h5(GSM3892578_SKIN_HV1_F2_filtered_gene_bc_matrices_h5.h5)

Error in Read10X_h5(GSM3892578_SKIN_HV1_F2_filtered_gene_bc_matrices_h5.h5) :  Please install hdf5r to read HDF5 files ###显示要安装包

        install.packages('hdf5r')

        library(hdf5r)

        h1= Read10X_h5(GSM3892578_SKIN_HV1_F2_filtered_gene_bc_matrices_h5.h5)

        #再用creatseuratobject函数创建seurat对象就可以了

        HC_1 <- CreateSeuratObject(counts = hc1, project = "HC_1", min.cells = 3, min.features = 200)

HC1就是一个seurat对象啦，再开启下游分析。