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Perform Timer Transformation on Flow Cytometry Data

Source: R/TockyDataPreprocessing.R
timer_transform.Rd

This function processes flow cytometry data by applying Timer thrsholding, normalization, and trigonometric transformation to the Blue and Red fluorescence data.

Usage

timer_transform(
  prep,
  select = TRUE,
  blue_channel = NULL,
  red_channel = NULL,
  normalization_method = "MAD",
  red_threshold = NULL,
  blue_threshold = NULL,
  interactive_gating = FALSE,
  verbose = TRUE,
  q = 0.998,
  normalization = TRUE
)

Arguments

prep

A list containing file paths and variables, typically the output from prep_tocky.

select

Logical indicating whether to choose Timer fluorescence channels interactively. Default is `TRUE`.

blue_channel

Character string specifying the Blue fluorescence channel name. If `NULL`, the function attempts to determine it automatically.

red_channel

Character string specifying the Red fluorescence channel name. If `NULL`, the function attempts to determine it automatically.

normalization_method

Charcter string specifying the normalization method to be applied to Timer flfuorescence Default is `MAD`. The alternative is `SD`.

red_threshold

Numeric specifying the Red channel gating threshold. If `NULL`, gating is performed automatically or interactively based on `interactive_gating`.

blue_threshold

Numeric specifying the Blue channel gating threshold. If `NULL`, gating is performed automatically or interactively based on `interactive_gating`.

interactive_gating

Logical indicating whether to perform interactive gating when thresholds are not provided. Default is `FALSE`.

verbose

Logical indicating whether to print progress messages. Default is `TRUE`.

q

Quantile value used for automatic Timer thresholds. Default is 0.998.

normalization

Logical indicating whether to apply Timer fluorescence normalization. Default is `TRUE`.

Value

The function returns a new TockyPrepData object containing:

  • Data: Data frame with angle, intensity, and other variables.

  • normalization_parameters: List with normalization values and coefficients.

  • cell_counts: Data frame with cell counts for each sample.

  • sampledef: Data frame with sample file names and placeholder group column.

Examples

if (FALSE) { # \dontrun{
  # Assuming `prep_data` is the output from `prep_tocky`
  result <- timer_transform(prep_data)
} # }