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# Export Flow Cytometry Dataset as SCE.

Source: `R/data_load_and_transform.R`
`export_sce.Rd`

This function creates an object of the class Single Cell Experiment (SCE) based on the data of the flow cytometry dataset (fcd).

## Usage

    export_sce(
      fcd = condor,
      expr_slot = "orig",
      reduction_method = NULL,
      reduction_slot = NULL,
      cluster_slot = NULL,
      cluster_var = NULL,
      save = TRUE,
      dir = paste0(getwd(), "/"),
      filename = ""
    )

## Arguments

fcd

  flow cytometry data set

expr_slot

  expr_slot from which to take marker expression values, default is "orig".

reduction_method

  string specifying which dimensionality reduction method to use.

reduction_slot

  string specifying reduction name in reduction_method to use for visualization, e.g. "pca_orig".

cluster_slot

  string specifying which clustering slot to use to find variable specified in cluster_var.

cluster_var

  string specifying variable name in cluster_slot that identifies cell population labels to be used (e.g. clusters, metaclusters or predicted labels). Must be numeric in this function - factors are converted automatically.

save

  boolean indicating if the sce should be saved as RDS file.

dir

  string specifying the directory where the RDS file is saved. Current working directory by default.

filename

  string specifying the filename for the RDS file.

## Value

The SCE plus a short message if the RDS file was saved successfully.

## Details

Save the results from cyCONDOR as a Single Cell Experiment Class as RDS file