morphology_corr.earth: Corrects morphology using multivariate adaptive regression...

In bjreisman/DebarcodeR: Automated Demultiplexing for Fluorescent Cell Barcoding

Corrects morphology using multivariate adaptive regression splines as implemented in the earth pacakge

Description

Corrects morphology using multivariate adaptive regression splines as implemented in the earth pacakge

Usage

morphology_corr.earth(
  fcb,
  uptake,
  ret.model = FALSE,
  what = c("x", "x + se"),
  nfold = 1,
  ncross = 0,
  channel,
  predictors = c("FSC-A", "SSC-A"),
  subsample = 30000,
  updateProgress = NULL,
  ...
)

Arguments

fcb	the barcoded dataframe, post compensation and preprocessing
uptake	Optional: a dataframe consisting of all cells barcoded with a single level of the barcoding dye
channel	The name (string) of the channel to be corrected, ie. the column name in 'fcb_df'
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.
updateProgress	used in reactive context (shiny) to return progress information to GUI#'

Value

a tibble/data.frame with the selected channel corrected for fsc and ssc

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