cytofin_homogenize: Homogenize CyTOF channels names using a consensus antigen...

In bennyyclo/Cytofin: Integrate CyTOF Datasets From Heterogeneous Sources

Description

This function homogenizes CyTOF data (.fcs files) from heterogeneous sources according to the standard panel in a .csv file located at panel_path.

Usage

cytofin_homogenize(
  metadata_path,
  panel_path,
  input_data_path,
  output_data_path,
  prefix = "homogenized_",
  verbose = FALSE
)

Arguments

metadata_path	A file path leading to an .xlsx or .csv file containing a table of CyTOF file (.fcs file) names in the first column (filename) and additional information about each .fcs file in subsequent columns. Columns should include filename, cohort, plate_number, patient_id, condition, is_anchor, and validation.
panel_path	A file path leading to an .xlsx or .csv file containing a table of standardized antigen panel information. Columns should include metal_name, antigen_name, antigen_pattern, lineage, functional, and general.
input_data_path	A folder directory containing the input .fcs files to be homogenized.
output_data_path	A folder directory to which the output (i.e. homogenized) .fcs files should be written.
prefix	A string appended to the name of each input file to create the name of the corresponding output file (post-homogenization). Defaults to "homogenized_" (e.g. an input file named "file1.fcs" will correspond to the output file "homogenized_file1.fcs" saved in output_data_path).
verbose	A boolean value indicating whether progress message should be printed to the console during homogenization. Defaults to FALSE.

Value

cytofin_homogenize doesn't return anything. Instead, it has the side-effect of saving homogenized files (in .fcs format) to the directory specified with output_data_path. Each of the saved files will contain homogenized, user-defined channels according to details specified in the file at panel_path.

bennyyclo/Cytofin documentation built on July 18, 2021, 8:16 a.m.