Converts an in-memory scMethrix to an HDF5 scMethrix

Source: R/scmethrix_operations.R

Converts an in-memory scMethrix to an HDF5 scMethrix

convert_scMethrix(scm = NULL, h5_dir = NULL, 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
verbose

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

Value

An object of class scMethrix, HDF5 format

Details

Takes a scMethrix object and returns with the same object with delayed array assay slots with HDF5 backend. Might take long time!

Examples

data('scMethrix_data')
convert_scMethrix(scMethrix_data, h5_dir=paste0(tempdir(),"/h5"))

#> 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 0.15s
#> Converted in [unknown time]
#> An object of class scMethrix
#>    n_CpGs: 286
#>    n_samples: 4
#>    assays: score, counts
#>    reduced dims: 
#>    is_h5: TRUE
#>    Reference: hg19
#>    Physical size: 37 Kb