openCyto (version 1.10.3)

quantileGate: 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

quantileGate(fr, channel, probs = 0.999, plot = FALSE, positive = TRUE,
  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

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)

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

gate <- quantileGate(fr, Channel = "APC-A", probs = 0.995) # fr is a flowFrame