Saves an HDF5 scMethrix object

Source: R/scmethrix_operations.R

Saves an HDF5 scMethrix object

save_HDF5_scMethrix(
  scm = NULL,
  h5_dir = NULL,
  replace = FALSE,
  verbose = TRUE,
  ...
)

Arguments

scm

scMethrix; the single cell methylation experiment
h5_dir

string; The directory to use. Will be created if it does not exist. Default = NULL
replace

Should it overwrite the pre-existing data? FALSE by default.
verbose

boolean; Flag for outputting function status messages. Default = TRUE
...

Parameters to pass to saveHDF5SummarizedExperiment

Value

Nothing

Details

Takes scMethrix object and saves it in the specified directory

Examples

data('scMethrix_data')
dir <- paste0(tempdir(),"/h5")
scm <- convert_scMethrix(scMethrix_data, h5_dir=dir)

#> Converting in-memory scMethrix to HDF5
#> Saving HDF5 experiment to disk...
#> Start writing assay 1/2 to HDF5 file:
#>   /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//Rtmpa5ljoK/h5/assays.h5
#> / Reading and realizing block 1/1 ... 
#> OK
#> \ Writing it ... 
#> OK
#> Finished writing assay 1/2 to HDF5 file:
#>   /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//Rtmpa5ljoK/h5/assays.h5
#> Start writing assay 2/2 to HDF5 file:
#>   /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//Rtmpa5ljoK/h5/assays.h5
#> / Reading and realizing block 1/1 ... 
#> OK
#> \ Writing it ... 
#> OK
#> Finished writing assay 2/2 to HDF5 file:
#>   /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//Rtmpa5ljoK/h5/assays.h5
#> Serialize SingleCellExperiment object to RDS file:
#>   /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//Rtmpa5ljoK/h5/se.rds
#> Experiment saved in 0.17s
#> Converted in [unknown time]
save_HDF5_scMethrix(scm, h5_dir = dir, replace = TRUE)

#> Saving HDF5 experiment to disk...
#> Start writing assay 1/2 to HDF5 file:
#>   /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//Rtmpa5ljoK/h5/assays.h5
#> / Reading and realizing block 1/1 ... 
#> OK
#> \ Writing it ... 
#> OK
#> Finished writing assay 1/2 to HDF5 file:
#>   /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//Rtmpa5ljoK/h5/assays.h5
#> Start writing assay 2/2 to HDF5 file:
#>   /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//Rtmpa5ljoK/h5/assays.h5
#> / Reading and realizing block 1/1 ... 
#> OK
#> \ Writing it ... 
#> OK
#> Finished writing assay 2/2 to HDF5 file:
#>   /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//Rtmpa5ljoK/h5/assays.h5
#> Serialize scMethrix object to RDS file:
#>   /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//Rtmpa5ljoK/h5/se.rds
#> Experiment saved in 0.21s