wsp_get_gs: Get (subsetted) gatingsets from flowjo workspaces

In Close-your-eyes/fcexpr: Complement the manual analysis of flow cytometric experiments and organize your fcs files in a consistent way

Get (subsetted) gatingsets from flowjo workspaces

Description

Get (subsetted) gatingsets from flowjo workspaces

Usage

wsp_get_gs(
  wsp,
  FCS.file.folder = NULL,
  groups = NULL,
  invert_groups = F,
  samples = NULL,
  invert_samples = F,
  remove_redundant_channels = F,
  lapply_fun = lapply,
  split_size = 2,
  additional.sampleID = F,
  ...
)

Arguments

wsp	vector of paths to flowjo workspaces
FCS.file.folder	path to folder(s) of FCS files; may be one path for all wsp or a vector of paths, one for each wsp; if not provided (NULL) fcs file paths are derived individually from wsps (xml)
groups	vector or list of groups in flowjo to consider; if a list, each index corresponds to the index in wsp; if NULL samples from all groups are read
invert_groups	logical whether to invert group selection
samples	vector or list of samples to select (names of FCS files), each index corresponds to the index in wsp; if NULL all samples (from selected groups) are read
invert_samples	logical whether to invert sample selection
remove_redundant_channels	remove channels that are not part of the gating tree, mainly to reduce memory load
lapply_fun	function name without quotes; lapply, pbapply::pblapply or parallel::mclapply are suggested
split_size	chunk size of splits of fcs files parsed to CytoML::flowjo_to_gatingset; splitting allows to have a progress bar from pblapply or to use multicore processing by parallel::mclapply
...	additional argument to the lapply function; mainly mc.cores when parallel::mclapply is chosen

Value

list of gatingsets

Examples

## Not run: 
gs_list <- fcexpr::wsp_get_gs(wsp = "mypath/my.wsp")

## End(Not run)

Close-your-eyes/fcexpr documentation built on Sept. 29, 2023, 12:27 a.m.