the single cell seurat object store in mongodb in R environment issue
honghh2018 opened this issue · 0 comments
Hi developer,
Thanks for the great tools to manipulate the mongod
Here is my problem:
how to insert the object data (size 1Gb) into the mongo using R script package mongolite
code below:
library(mongolite)
data <- readRDS("hg19_seurat.rds")
binary_data <- serialize(data, NULL)
mongo_con <- mongo(collection = "seurat_col", db = "seurat_db", url = "mongodb://127.0.0.1")
gridfs_id <- mongo_con$gridfs$put(data = binary_data, filename = "seurat_data")
mongo_con$disconnect()
mongo_con <- mongo(collection = "seurat_col", db = "seurat_db", url = "mongodb://127.0.0.1")
binary_data1 <- mongo_con$gridfs$get(gridfs_id)$read()
seurat_obj1 <- unserialize(binary_data1)
identical(data, seurat_obj1)
the above code show me error
can not get the object "binary_data1"
how can i fix this issue?
any advice would be appreciated.
Best,
hanhuihong