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run_cytonorm

Source: R/batch_correction.R
run_cytonorm.Rd

Wrapper function around CytoNorm.normalize from the CytoNorm package.

Usage

run_cytonorm(
  fcd,
  batch_var,
  keep_fcs = TRUE,
  output_dir = paste0("./CytoNorm_output_", Sys.Date()),
  files = NULL,
  data_path = NULL,
  anno_table = NULL
)

Arguments

fcd

flow cytometry dataset

batch_var

Column name of batch variable from fcd$anno$cell_anno.

keep_fcs

Boolean whether to keep the normalized FCS files in output_dir.

output_dir

Directory to save normalized FCS files temporary or permanently, if keep_fcs == TRUE.

files

Vector of fcs file names of samples which should be normalized. By default all files contained in the flow cytometry dataset are used.

data_path

File path to folder where .fcs files contained in the fcd are stored.

anno_table

Path to the annotation table file.

Value

fcd with a normalized expression data frame saved in fcd$expr$norm.

Details

run_cytonorm

This function assumes that your fcd contains a trained model computed by train_cytonorm. The function performs normalization of the samples contained in your fcd. The normalized expression values are added to your fcd and by default FCS files with the normalized values are written to the output_dir. See [Van Gassen et al., 2019](https://doi.org/10.1002/cyto.a.23904) for more details on CytoNorm.