export.metaFCS: Create FCS from a 'fcs.SCE' object

In jgarces02/FlowCT: A semi-automated workflow for deconvolution of immunophenotypic data and objective reporting on large datasets

Create FCS from a fcs.SCE object

Description

It creates a FCS file containing all analysis incorpored to colData(fcs.SCE) as well as the dimensional reduction coordinates calculated.

Usage

export.metaFCS(
  fcs.SCE,
  assay.i = "raw",
  output.name = NULL,
  output.folder = getwd(),
  separate.fcs = FALSE,
  output.suffix = "meta"
)

Arguments

fcs.SCE	A fcs.SCE object generated through FlowCT::fcs.SCE().
output.name	Name for generated FCS file. If NULL (default), the project name specified in the fcs.SCE building will be used.
output.folder	Name of the folder within store the new generated FCS files. Default = getwd() (i.e., current directory).
separate.fcs	Logical indicating whether FCS must be exporting separatelly or not. Default = FALSE.
output.suffix	Suffix to be added to the new generated FCS files. Default = "meta".
dr.object	Object created with FlowCT::dim.reduction() function or a table combining DR and experimental metadata information.

Examples

## Not run: 
# option 1: save entire analysis as a single FCS file
export.metaFCS(fcs.SCE = fcs, output.name = "final_analysis")

# option 2: save separatelly each file contained within the fcs.SCE object
export.metaFCS(fcs.SCE = fcs, separate.fcs = T, output.suffix = "meta.final")

## End(Not run)

jgarces02/FlowCT documentation built on March 28, 2023, 12:42 p.m.