gate_mindensity2: An improved version of mindensity used to determines a...

In openCyto: Hierarchical Gating Pipeline for flow cytometry data

Description

Analogous to the original openCyto::mindensity(), mindensity2 operates on a standard flowFrame. Its behavior is closely modeled on the original mindensity() whenever possible. However, the underlying peak-finding algorithm (improvedMindensity) behaves significantly differently.

Usage

gate_mindensity2(
  fr,
  channel,
  filterId = "",
  pivot = FALSE,
  gate_range = NULL,
  min = NULL,
  max = NULL,
  peaks = NULL,
  ...
)

Arguments

fr	a flowFrame object
channel	the channel to operate on
filterId	a name to refer to this filter
pivot	logical value. If TRUE, we choose as the two peaks the largest peak and its neighboring peak. See details.
gate_range	numeric vector of length 2. If given, this sets the bounds on the gate applied.
min	a numeric value that sets the lower boundary for data filtering
max	a numeric value that sets the upper boundary for data filtering
peaks	numeric vector. If not given , then perform peak detection first by .find_peaks
...	Additional arguments for peak detection.

Value

a rectangleGate object based on the minimum density cutpoint

Author(s)

Greg Finak, Phu T. Van

Examples

## Not run: 
 gate <- gate_mindensity2(fr, channel = "APC-A") # fr is a flowFrame

## End(Not run)

openCyto documentation built on Nov. 8, 2020, 5:40 p.m.