save_faust_pop: Save FAUST subset as an FCS file

Description Usage Arguments Value Examples

View source: R/save_faust_pop.R

Description

Save a specified FAUST-identified population to project_path/faustData/fcsData as an FCS file for all samples gated or just a specified subset.

Usage

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save_faust_pop(
  project_path,
  pop,
  fr_source = NULL,
  sample = NULL,
  trans_fn = NULL,
  trans_chnl = NULL
)

Arguments

project_path

character. FAUST project directory.

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.

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

integer vector or character vector. If an integer vector, then it specifies the indices of the samples for which to save output. If character, then it specifies the names of the sames to save output for. If NULL, then the output for every sample is saved. Default is NULL.

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). Side effect is the saved FCS file.

Examples

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save_faust_pop(project_path = "", pop = list("CD3" = 2),
gs = gs, sample = 1)

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