gate_quad_tmix: quadGate based on flowClust::tmixFiler

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

quadGate based on flowClust::tmixFiler

Description

This gating method identifies two quadrants (first, and third quadrants) by fitting the data with tmixture model. It is particually useful when the two markers are not well resolved thus the regular quadGate method based on 1d gating will not find the perfect cut points on both dimensions.

Usage

gate_quad_tmix(
  fr,
  channels,
  K,
  usePrior = "no",
  prior = list(NA),
  quantile1 = 0.8,
  quantile3 = 0.8,
  trans = 0,
  plot = FALSE,
  ...
)

Arguments

fr	flowFrame
channels	character vector specifies two channels
K	see gate_flowclust_2d
usePrior	see gate_flowclust_2d
prior	see gate_flowclust_2d
quantile1	numeric specifies the quantile level(see 'level' in flowClust) for the first quadrant (x-y+)
quantile3	numeric specifies the quantile level see 'level' in flowClust for third quadrant (x+y-)
trans	see gate_flowclust_2d
plot	logical whether to plot flowClust clustering results
...	other arguments passed to flowClust

Value

a filters object that contains four polygonGates following the order of (-+,++,+-,–)

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