R语言：读取loom文件，以及loom文件转成Seurat对象

使用satijalab开发的loomR读取loom文件，具体详见https://satijalab.org/loomr/loomr_tutorial

library(loomR) #

lfile <- connect(filename = "osmFISH_SScortex_mouse_all_cells.loom", mode = "r+")
lfile
lfile$matrix
full.matrix <- lfile$matrix[, ]
dim(x = full.matrix)


A <-lfile$col.attrs$CellID[]
B <-lfile$col.attrs$ClusterName[] 
C <-lfile$col.attrs$ClusterID[]

D <-lfile$row.attrs$Gene[]


#############转成Seurat对象的方式##############
full.matrix <- lfile$matrix[,]
dim(full.matrix)
full.matrix <- t(full.matrix)
gene_name <- lfile$row.attrs$Gene[] #基因名
barcode <- lfile$col.attrs$CellID[] #细胞ID

colnames(full.matrix) <- barcode
rownames(full.matrix) <-gene_name

S =CreateSeuratObject(counts = full.matrix,project = 'SP',min.cells = 0, min.features = 0)
S$ClusterID  <- lfile$col.attrs$ClusterID[]
S$ClusterName <- lfile$col.attrs$ClusterName[]
S$Regin <- lfile$col.attrs$Region[]
S$Total_molecules  <- lfile$col.attrs$Total_molecules[]
S$Valid <- lfile$col.attrs$Valid[]
S$X         <- lfile$col.attrs$X[]
S$Y <-lfile$col.attrs$Y[]
S$size_pix <- lfile$col.attrs$size_pix[]
S$size_um2 <- lfile$col.attrs$size_um2[]

S@assays$RNA@meta.features$Fluorophore <- lfile$row.attrs$Fluorophore[]
S@assays$RNA@meta.features$Hybridization <- lfile$row.attrs$Hybridization[]

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