Get (subsetted) gatingsets from flowjo workspaces

wsp_get_gs(
  wsp,
  FCS.file.folder = NULL,
  groups = NULL,
  invert_groups = F,
  samples = NULL,
  invert_samples = F,
  remove_redundant_channels = 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

Value

list of gatingsets

Examples

if (FALSE) {
gs_list <- fcexpr::wsp_get_gs(wsp = "mypath/my.wsp")
}