R Notebook

Load the libraries

print("Hello World")

[1] "Hello World"

Notice that “first-trimester-decidua-human-placenta-10XV2.loom” is already analyzed, and we already created the Seurat Object.

loom_obj1 <- Connect(filename = "first-trimester-decidua-human-placenta-10XV2.loom",
                    mode = 'r')

seurat_loom1 <- as.Seurat(loom_obj1)
saveRDS(seurat_loom, "seuratObj.rds")

dim(sSeurat1)

Error: object 'sSeurat1' not found

Continue for the other 3 loom files

seurat_loom2 <- as.Seurat(loom_obj2)

Reading in /matrix
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 't': cannot allocate vector of size 68.3 Gb

seurat_loom2 <- LoadLoom("4584e785-dc1d-4f31-99ca-76626fe7e2bf.loom",
                        
saveRDS(seurat_loom2, "seuratObj2.rds")

sSeurat2 <- readRDS("seuratObj2.rds")

cannot open compressed file 'seuratObj2.rds', probable reason 'No such file or directory'Error in gzfile(file, "rb") : cannot open the connection

Keep going for the third loom file

seurat_loom3 <- as.Seurat(loom_obj3)

Reading in /matrix
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 't': cannot allocate vector of size 170.9 Gb

sSeurat3 <- readRDS("seuratObj3.rds")
dim(sSeurat3)

Finally, the last loom file

loom_obj4 <- Connect(filename = "c0d33f68-1573-45d2-9295-7f93f9a086b0.loom",
                    mode = 'r')

seurat_loom4 <- as.Seurat(loom_obj4)

Reading in /matrix
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 't': cannot allocate vector of size 198.4 Gb

sSeurat4 <- readRDS("seuratObj4.rds")
dim(sSeurat4)