Initialize an odm object

initialize_odm_from_backing_file() initializes an odm object from a backing .odm file.

Usage

initialize_odm_from_backing_file(odm_file)

Arguments

odm_file

file path to a backing .odm file.

Value

an odm object

Details

initialize_odm_from_backing_file() is portable: the user can create an .odm file (via create_odm_from_cellranger() or create_odm_from_r_matrix()) on one computer, transfer the .odm file to another computer, and then load the .odm file (via initialize_odm_from_backing_file()) on the second computer.

Examples

library(sceptredata)
directories_to_load <- paste0(
 system.file("extdata", package = "sceptredata"),
 "/highmoi_example/gem_group_", c(1, 2)
)
directory_to_write <- tempdir()
out_list <- create_odm_from_cellranger(
  directories_to_load = directories_to_load,
  directory_to_write = directory_to_write,
)
#> Round 1/2 processing of the input files.
#> 	Processing file 1 of 2.
#> 	Processing file 2 of 2.
#> Round 2/2 processing of the input files.
#> 	Processing file 1 of 2. Computing cellwise covariates. Writing to disk.
#> 	Processing file 2 of 2. Computing cellwise covariates. Writing to disk.
gene_odm <- out_list$gene
gene_odm
#> An object of class odm with the following attributes:
#> 	• 526 features
#> 	• 45919 cells
#> 	• Backing file: /var/folders/7v/5sqjgh8j28lgf8qx3gbtq1h00000gp/T//Rtmp8pBZJd/gene.odm

# delete the gene_odm object
rm(gene_odm)

# reinitialize the gene_odm object
gene_odm <- initialize_odm_from_backing_file(
  paste0(tempdir(), "/gene.odm")
)
gene_odm
#> An object of class odm with the following attributes:
#> 	• 526 features
#> 	• 45919 cells
#> 	• Backing file: /var/folders/7v/5sqjgh8j28lgf8qx3gbtq1h00000gp/T//Rtmp8pBZJd/gene.odm