gate_quantile: Determine the cutpoint by the events quantile.

In RGLab/openCyto: Hierarchical Gating Pipeline for flow cytometry data

Determine the cutpoint by the events quantile.

Description

It is possible that the cutpoint calculated by quantile function may not produce the exact the probability set by 'probs' argument if there are not enough cell events to reach that precision. Sometime the difference could be significant.

Usage

gate_quantile(
  fr,
  channel,
  probs = 0.999,
  plot = FALSE,
  filterId = "",
  min = NULL,
  max = NULL,
  ...
)

Arguments

fr	a flowFrame object
channel	the channel from which the cytokine gate is constructed
probs	probabilities passed to 'stats::quantile' function.
plot	whether to plot the gate result
filterId	the name of the filter
min	a numeric value that sets the lower boundary for data filtering
max	a numeric value that sets the upper boundary for data filtering
...	additional arguments passed to 'stats::quantile' function.

Value

a rectangleGate

Examples

## Not run: 
 gate <- gate_quantile(fr, Channel = "APC-A", probs = 0.995) # fr is a flowFrame

## End(Not run)

RGLab/openCyto documentation built on Nov. 7, 2024, 9:23 p.m.