morphology_corr: Corrects morphology based on scatter or uptake control.

In bjreisman/DebarcodeR: Automated Demultiplexing for Fluorescent Cell Barcoding

Corrects morphology based on scatter or uptake control.

Description

Corrects morphology based on scatter or uptake control.

Usage

morphology_corr(
  fcb,
  uptake = NULL,
  channel,
  method = c("earth", "knijnenburg", "lm"),
  predictors = c("FSC-A", "SSC-A"),
  subsample = 20000,
  ret.model = TRUE,
  verbose = FALSE,
  ...
)

Arguments

channel	The name (string) of the channel to be corrected, ie. the column name in 'fcb_df'
subsample	Integer, number of cells to sample (with replacement) for the morphology correction, defaults to 10,000.
fcb_df	the barcoded dataframe, post compensation and preprocessing
bc_single_level	Optional: a dataframe consisting of all cells barcoded with a single level of the barcoding dye
opt	String, Morphology correction apporach, either "regression" (default) or "control dye"
trans	String, transformation to apply to the barcoding channels, defaults to arcsinh, also log10
updateProgress	used in reactive context (shiny) to return progress information to GUI
cofactor_bc1	Numeirc, Cofactor used for the arcsinh transformation on the barcoding channels
cofactor_update	Numeric, Cofactor used for the arcsinh transformation of the uptake channel
uptake_channel	String, uptake channel if "control dye" option is used as morphology correction method
output	what to return

Value

numeric vector of length nrow(fcb_df) representing the morphology corrected channel or a list containing the vector and the model used to correct it.

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