rliger (version 2.0.1)

restoreH5Liger: Restore links (to HDF5 files) for reloaded liger/ligerDataset object

Description

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)

Value

object with restored links.

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.

Examples

h5Path <- system.file("extdata/ctrl.h5", package = "rliger")
tempPath <- tempfile(fileext = ".h5")
file.copy(from = h5Path, to = tempPath)
lig <- createLiger(list(ctrl = tempPath))
# 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)
lig <- restoreH5Liger(lig)