Save the results from cyCONDOR as FCS file(s)

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)