save_gs: save/load a GatingSet/GatingSetList to/from disk.

In flowWorkspace: Infrastructure for representing and interacting with gated and ungated cytometry data sets.

Description

Save/load a GatingSet/GatingSetList which is the gated flow data including gates and populations to/from the disk. The GatingSet object The internal C data structure (gating tree),ncdfFlowSet object(if applicable)

Retrieve sample names by scanning h5 files from a GatingSet folder

Usage

save_gs(
  gs,
  path,
  cdf = NULL,
  backend_opt = c("copy", "move", "skip", "symlink", "link"),
  cred = NULL,
  ...
)

load_gs(
  path,
  h5_readonly = NULL,
  backend_readonly = TRUE,
  select = character(),
  verbose = FALSE,
  cred = NULL
)

## S4 method for signature 'character'
sampleNames(object)

save_gslist(gslist, path, ...)

load_gslist(path)

Arguments

gs	A GatingSet
path	A character scalar giving the path to save/load the GatingSet to/from.
backend_opt	a character scalar. The valid options are :"copy","move","skip","symlink" specifying what to do with the backend data file. Sometimes it is more efficient to move or create a symlink of the existing backend file to the archived folder. It is useful to "skip" archiving backend file if raw data has not been changed.
cred	credentials for s3 access. It is a list containing elements of "AWS_ACCESS_KEY_ID", "AWS_SECRET_ACCESS_KEY", "AWS_REGION" when NULL, read the default credential file from disk (e.g., ~/.aws/credentials)
...	other arguments: not used.
h5_readonly	whether to open h5 data as read-only. Default is TRUE
select	an integer or character vector to select a subset of samples to load
verbose	logical flag to optionally print the versions of the libraries that were used to archive the GatingSet for troubleshooting purpose.
object	a GatingSet folder
gslist	A GatingSetList

See Also

GatingSet-class,GatingSetList-class

Examples

## Not run: 
	#G is a GatingSet
	save_gs(G,path="tempFolder")
	G1<-load_gs(path="tempFolder")

	#G is a GatingSet

	save_gslist(gslist1,path="tempFolder")
	gslist2<-load_gslist(path="tempFolder")

## End(Not run)
      ## Not run: 
        sampleNames(gsdir)
      
## End(Not run)

flowWorkspace documentation built on Nov. 8, 2020, 8:08 p.m.