Perform Quality Control on Flow Cytometry Data using PeacoQC

This function performs quality control on flow cytometry data using the PeacoQC method. It transforms the data, removes margins, and identifies good cells. The function also optionally plots the results and saves the cleaned data.

do.peacoQC(
  dirty.expr,
  sample.name,
  spectral.channel,
  biexp.transform,
  transform.inv,
  output.dir,
  time.param,
  all.channels,
  method = "MAD",
  figures = TRUE,
  verbose = TRUE
)

Arguments

dirty.expr

A matrix containing the raw expression data, pre-cleaning.

sample.name

The name of the sample.

spectral.channel

The spectral channels to be used.

biexp.transform

The biexponential transformation function.

transform.inv

The inverse transformation function.

output.dir

The directory to save output files.

time.param

The time channel parameter.

all.channels

A vector of all channels to be included in the final cleaned data.

method

The PeacoQC method to use. Inherited from PeacoQC. Options are all, MAD or IT. Default is MAD.

figures

Logical. Controls whether PeacoQC plots are created. Default is TRUE.

verbose

Logical, default is TRUE. Set to FALSE to suppress messages.

Value

A matrix with the cleaned expression data.