Export Flow Cytometry Dataset as SCE. — export

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