openCyto (version 1.10.3)

tailgate: Gates the tail of a density using the derivative of a kernel density estimate

Description

Gates the tail of a density using the derivative of a kernel density estimate

Usage

tailgate(fr, channel, filterId = "", num_peaks = 1, ref_peak = 1,
  strict = TRUE, tol = 0.01, positive = TRUE, side = "right",
  min = NULL, max = NULL, ...)
cytokine(fr, channel, filterId = "", num_peaks = 1, ref_peak = 1,
  tol = 0.01, positive = TRUE, side = "right", ...)

Arguments

fr

a flowFrame object

channel

the channel from which the cytokine gate is constructed

filterId

the name of the filter

num_peaks

the number of peaks expected to see. This effectively removes any peaks that are artifacts of smoothing

ref_peak

After num_peaks are found, this argument provides the index of the reference population from which a gate will be obtained.

strict

logical when the actual number of peaks detected is less than ref_peak. an error is reported by default. But if strict is set to FALSE, then the reference peak will be reset to the peak of the far right.

tol

the tolerance value used to construct the cytokine gate from the derivative of the kernel density estimate

positive

If TRUE, then the gate consists of the entire real line to the right of the cutpoint. Otherwise, the gate is the entire real line to the left of the cutpoint. (Default: TRUE)

side

On which side of the density do we want to gate the tail, the 'right' (default) or 'left'?

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.

Value

• a filterList containing the gates (cutpoints) for each sample

Examples

gate <- tailgate(fr, Channel = "APC-A") # fr is a flowFrame