wsp_get_indices: Get indices for all gated populations in a flowjo workspace

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

Get indices for all gated populations in a flowjo workspace

Description

Every row in a fcs file represents an event. Every column is a parameter (channel). Gates select a subset (rows) of events by applying limits to usually one or two channels. A sub-population of gated events hence may be defined by a vector of (row-) indices (TRUE - events is included in gate; FALSE - event is not included). A whole gating tree may be represented by a matrix with n columns for n gates and m rows for m events. The output of this function may be saved to disk and applied to fcs files with fcexpr::inds_get_ff in order to obtain subsetted flowfframes representing gated populations in flowjo.

Usage

wsp_get_indices(
  wsp,
  FCS.file.folder = NULL,
  groups = NULL,
  invert_groups = F,
  samples = NULL,
  invert_samples = F,
  lapply_fun = lapply,
  ...
)

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
lapply_fun	lapply function name, unquoted; lapply, pbapply::pblapply or parallel::mclapply are suggested
...	additional argument to the lapply function; mainly mc.cores when parallel::mclapply is chosen

Details

Geometric gate definitions from flowjo are applied with CytoML::flowjo_to_gatingset and indices matrices are obtained with flowWorkspace::gh_pop_get_indices_mat. This process may take a while depend upon size of fcs files as a .h5 file is written to disk for every fcs file before indices can be derived. Hence, it is recommended to save the indices-matrices to disk in case of large FCS files.

Value

list of matrices, one for each selected sample; each column of the matrices holds the indices for the respective population

Examples

## Not run: 
ind_mat <- fcexpr::wsp_get_indices("mypath/my.wsp")

## End(Not run)

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