Restore links (to HDF5 files) for reloaded liger/ligerDataset object

When loading the saved liger object with HDF5 data in a new R session, the links to HDF5 files would be closed. This function enables the restoration of those links so that new analyses can be carried out.

Usage

restoreH5Liger(object, filePath = NULL)

restoreOnlineLiger(object, file.path = NULL)

Arguments

object: liger or ligerDataset object.
filePath: Paths to HDF5 files. A single character path for ligerDataset input or a list of paths named by the datasets for liger object input. Default NULL looks for the path(s) of the last valid loading.
file.path: Will be deprecated with restoreOnlineLiger. The same as filePath.

Value

object with restored links.

Note

restoreOnlineLiger will be deprecated for clarifying the terms used for data structure.

Examples

h5Path <- system.file("extdata/ctrl.h5", package = "rliger")
tempPath <- tempfile(fileext = ".h5")
file.copy(from = h5Path, to = tempPath)
#> [1] TRUE
lig <- createLiger(list(ctrl = tempPath))
#> Found more than one class "H5D" in cache; using the first, from namespace 'rliger'
#> Also defined by ‘hdf5r’
#> Found more than one class "H5D" in cache; using the first, from namespace 'rliger'
#> Also defined by ‘hdf5r’
#> Found more than one class "H5D" in cache; using the first, from namespace 'rliger'
#> Also defined by ‘hdf5r’
#> ! No human mitochondrial gene found in the union of dataset "ctrl"
#> ℹ calculating QC for dataset "ctrl"
#> 
#> ℹ Updated QC variables: "nUMI", "nGene", "mito", "ribo", and "hemo"
#> ℹ calculating QC for dataset "ctrl"

#> ✔ calculating QC for dataset "ctrl" ... done
#> 
# Now it is actually an invalid object! which is equivalent to what users
# will get with `saveRDS(lig, "object.rds"); lig <- readRDS("object.rds")``
closeAllH5(lig)
#> ℹ Closing H5 file: /private/var/folders/k9/nwtr_c_57kd43cmbtz82ywlr0000gn/T/Rtmp7iLTzn/filed38f3456de47.h5
lig <- restoreH5Liger(lig)
#> ℹ Restoring dataset "ctrl"
#> Found more than one class "H5D" in cache; using the first, from namespace 'rliger'
#> Also defined by ‘hdf5r’
#> ℹ Restoring HDF5 link from: /private/var/folders/k9/nwtr_c_57kd43cmbtz82ywlr000…
#> Found more than one class "H5D" in cache; using the first, from namespace 'rliger'
#> Also defined by ‘hdf5r’
#> Found more than one class "H5D" in cache; using the first, from namespace 'rliger'
#> Also defined by ‘hdf5r’
#> Found more than one class "H5D" in cache; using the first, from namespace 'rliger'
#> Also defined by ‘hdf5r’
#> ✔ Restoring HDF5 link from: /private/var/folders/k9/nwtr_c_57kd43cmbtz82ywlr000…
#> 
#> ℹ Restoring dataset "ctrl"

#> ✔ Restoring dataset "ctrl" ... done
#>