em_optimize: Defines populations on barcoded datasets

In bjreisman/DebarcodeR: Automated Demultiplexing for Fluorescent Cell Barcoding

Defines populations on barcoded datasets

Description

Defines populations on barcoded datasets

Usage

em_optimize(
  fcbFlowFrame,
  modelName = "VEE",
  subsample = 50000,
  verbose = TRUE,
  niter = 1,
  shrinkage = 0.05
)

Arguments

fcbFlowFrame	a fcbFlowFrame object with barcoded flowframe and uptake flowframe post deskewing, clustering, and assignment
subsample	number, number of cells to subsample during m step
ambiguitycut	numeric from 0 to 1, threshhold below which to discard ambigious cells, eg: 0.02, discards cells with more than 2% chance of originating from another population

Value

a fcbFlowFrame object with a barcode slot filled with deskewing, clustering, cell assignment as a vector of integers from 0:ncol(probs), cells assigned a classification of 0 remained unassigned, otherwise number corresponds to the barcoding level assignment of that cell

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