dot-save_faust_pop: Save FAUST subset as an FCS file

Description Usage Arguments Value

Description

Save FAUST subset as an FCS file

Usage

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.save_faust_pop(
  project_path,
  fr_source,
  sample_name,
  sel_sample,
  pop,
  dir_save,
  trans_fn = NULL,
  trans_chnl = NULL
)

Arguments

project_path

character. FAUST project directory.

fr_source

GatingSet or character vector. If a GatingSet, then the flowFrames within the GatingSet are used to create the output fcs files. If a character vector, then must specify a directory containing FCS files. These FCS files are used to create the output fcs files.

sample_name

character vector. Specifies names of samples in order in which they are found in gs.

sel_sample

character vector. Character vector specifying the names of the samples (as saved by FAUST as folder names in the analysis map and equivalent to gs[[i]]@name where i is an index in gs.) that are to have their FAUST pops saved.

pop

list or named character vector. If a character vector, then all cells matching the set of marker levels are returned. If a list, then each element must be a character vector, and then all cells matching either of these specified sets of marker levels are returned.

dir_save

character. Specifies directory in which files are saved.

trans_fn

function. If supplied, this function is applied to the expression data. Useful for back-transformation. If NULL, then no transformation is applied. Default is NULL.

trans_chnl

character vector. If specified, trans_fn is applied to only these channels. If NULL and if trans_fn is not NULL, then trans_fn is applied to entire expression matrix. Default is NULL.

Value

invisible(TRUE).


MiguelRodo/faustutils documentation built on March 26, 2021, 11:50 p.m.