deskew_fcbFlowSet: Corrects morphology based on scatter or uptake control for...

In bjreisman/DebarcodeR: Automated Demultiplexing for Fluorescent Cell Barcoding

Corrects morphology based on scatter or uptake control for fcbFlowFrame

Description

Corrects morphology based on scatter or uptake control for fcbFlowFrame

Usage

deskew_fcbFlowSet(
  fcbFlowSet,
  uptake = NULL,
  channel,
  method = "earth",
  predictors = c("fsc_a", "ssc_a"),
  subsample = 20000,
  ret.model = TRUE,
  verbose = FALSE,
  updateProgress = NULL,
  ...
)

Arguments

channel	The name (string) of the channel to be corrected, ie. the column name in fcbFlowFrame barcoded.ff exprs
method	The name of the morphology correction model to use. Choose between earth, lm (linear model), or knijnenburg
predictors	The vector of channel names to be used to build the regression model
subsample	Integer, number of cells to sample (with replacement) for the morphology correction, defaults to 10,000.
ret.model	Option to retain the model for deskewing
updateProgress	used in reactive context (shiny) to return progress information to GUI
fcbFlowFrame	a fcbFlowFrame object with barcoded flowframe and uptake flowframe, post compensation and preprocessing

Value

a fcbFlowFrame with barcode slots added for selected channel corrected for predictors chosen

bjreisman/DebarcodeR documentation built on Oct. 22, 2022, 1:50 a.m.