cytofin_prep_anchors: Prepare CyTOF controls for batch normalization across plates
In bennyyclo/Cytofin: Integrate CyTOF Datasets From Heterogeneous Sources

This function calculates reference statistics needed for CytofIn batch normalization. Specifically, it calculates the universal mean and universal variance vectors of the generalized anchors identified in the metadata file at metadata_path; in addition, it calculates the non-channel-specific bulk mean and bulk variance of the generalized anchors.

cytofin_prep_anchors(
  metadata_path,
  panel_path,
  input_data_path,
  input_prefix = "homogenized_",
  output_path = "none",
  shift_factor = 0,
  scale_factor = 0.2
)

`metadata_path`	A file path leading to an .xlsx or .csv file containing a table of CyTOF file (.fcs file) names. Columns should include `filename`, `cohort`, `plate_number`, `patient_id`, `condition`, `population`, and `validation`. See the vignette for details: `vignette("help", package = "cytofin")`
`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`. See the vignette for details: `vignette("help", package = "cytofin")`
`input_data_path`	A folder directory containing the input CyTOF files to be prepped for normalization. These files should already be homogenized, and in most cases this will be the directory to which the output .fcs files from `cytofin_homogenize` were written.
`input_prefix`	The string that was appended to the name of the input files of `cytofin_homogenize` to create their corresponding output file names. Defaults to "homogenized_".
`output_path`	A file path specifying where to save the output .rds file containing the statistics calculated from this step and the concatenated .FCS files containing all cells from the generalized anchor samples. Defaults to "none", in which case no files are saved.
`shift_factor`	The scalar value `a` in the following equation used to transform CyTOF raw data ion counts using the hyperbolic arc-sine function: `new_x <- asinh(a + b*x)`. Defaults to 0.
`scale_factor`	The scalar value `b` in the following equation used to transform CyTOF raw data ion counts using the hyperbolic arc-sine function: `new_x <- asinh(a + b*x)`. Defaults to 0.2.

a list() of summary statistics with the following elements:

universal_var: a named numeric vector in which each entry corresponds to the universal variance of an antigen channel in the homogenized dataset
universal_mean: a named numeric vector in which each entry corresponds to the universal mean of an antigen channel in the homogenized dataset
bulk_var: The mean of all the channel-specific universal variances in universal_var (a scalar value)
bulk_mean: The mean of all the channel-specific universal means in universal_mean (a scalar value)