deGate: A Fancy 1D Threshold Calculator

In rogerswt/wadeTools: Wade's Hodgepodge of Flow Cytometry Functions

A Fancy 1D Threshold Calculator

Description

Estimates the number of cell subsets and identifies the best threshold to gate the positive/negative subsets of cell populations in 1D. Note: This function was written by M. Jafar Taghiyar and included with his kind permission.

Usage

deGate(
  f,
  channel,
  n.sd = 1.5,
  high = FALSE,
  percentile,
  kernel = "gaussian",
  graphs = FALSE,
  all.cut = FALSE
)

Arguments

f	A flowFrame
channel	an integer to specifiy the channel for 1D density estimation analysis
n.sd	an integer that is multiplied to the standard deviation to determine the place of threshold
high	if TRUE, returns the 'percentile' threshold. It returns the 99th percentile by default
percentile	a value in the interval 0,1 that is used as the percentile is 'high' is TRUE
kernel	refer to the '?density' in r base
graphs	if TRUE, it plots the density as well as the threshold on the same plot
all.cut	if TRUE, it returns all the cutoff points whose length can roughly estiamte the number of cell subsets in that dimension

Value

cutoffs, i.e. thresholds on the 2D data

rogerswt/wadeTools documentation built on Feb. 16, 2023, 7:47 a.m.