inds_get_ff: Get (subsetted) flowFrames from FCS files

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

Get (subsetted) flowFrames from FCS files

Description

From a matrix of indices generated with fcexpr::wsp_get_indices flowframes are generated. Only those events within the selected population are included in flowframes. By default no compensation will be applied on fluorescence intensites. This can be done afterwards though with in appropriate compensation matrix.

Usage

inds_get_ff(
  ind_mat,
  population,
  alias_attr_name = "short_names",
  path_attr_name = "FilePath",
  downsample = 1,
  lapply_fun = lapply,
  seed = 42,
  channels = channels,
  leverage_score_for_sampling = F,
  ...
)

Arguments

ind_mat	a list of indices matrices, preferentially generated with fcexpr::wsp_get_indices
population	which population (=node, =gate) to subset flowFrames on; must be a column name of ind_mat or an alias stored in alias_attr_name
alias_attr_name	the name of attribute containing aliases (shortest unique names) of node-names (gating paths)
path_attr_name	the name of attribute containing the path (url) to the fcs file on which to apply the subsetting
downsample	numeric, if < 0 then a fraction of events is sampled, if > 0 an absolute number of events is sampled; or set to "min" which will lead to downsampling each flowframe to the number of events in the flowframe with lowest number of events; can be a single value to treat all FCS files equally or can be a vector of same length as FCS files
lapply_fun	lapply function name, unquoted; lapply, pbapply::pblapply or parallel::mclapply are suggested
seed	set a seed to reproduce downsampling
channels	channels to use for leverage score calculation; use wsx_get_keywords to retrieve channel names/descriptions
leverage_score_for_sampling	logical whether to use leverage scores for downsampling
...	additional argument to the lapply function; mainly mc.cores when parallel::mclapply is chosen as lapply_fun

Value

list of flow frames, one for each ind_mat

Examples

## Not run: 
ind_mat <- fcexpr::wsp_get_indices("mypath/my.wsp")
ff <- inds_get_ff(ind_mat = ind_mat, population = "CD8+")

## End(Not run)

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