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# Save the results from cyCONDOR as FCS file(s)

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

Saves the expression data, annotation data and (optionally) results from the cyCONDOR analysis (dimensionality reduction, clustering) as one or more FCS file(s).

## Usage

    write_fcs(
      fcd = condor,
      expr_slot = "orig",
      reduction_method = NULL,
      reduction_slot = NULL,
      cluster_slot = NULL,
      cluster_var = NULL,
      split_by = NULL,
      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.

split_by

  NULL or character string specifying a metadata variable (e.g. sample_ID) to split the data. If NULL, only one FCS file with all data is generated.

dir

  string specifying the directory where the FCS file(s) is/are saved. Current working directory by default.

filename

  string specifying the filename for the FCS file. If split_by is defined, an automatic suffix according to the defined variable is assigned to the FCS files.

## Value

Message that FCS file(s) are saved in the defined directory.

## Details

Save the results from cyCONDOR as FCS file(s)