Usage
deGate(flow.frame, channel, n.sd=1.5, use.percentile = FALSE,
percentile = 0.95, upper = NA, alpha = 0.1,
sd.threshold = FALSE, graphs = FALSE, all.cut = FALSE, tinypeak.removal=1/25)
Arguments
flow.frame
a 'FlowFrame' object.
channel
a channel's name or its corresponding index in the 'flow.frame'.
n.sd
an integer coefficient for the standard deviation
to determine the threshold based on the standard deviation if 'sd.threshold' is TRUE.
use.percentile
if TRUE, forces to return the 'percentile'th threshold.
percentile
a value in [0,1] that is used as the percentile. The default value is 0.95.
upper
if TRUE, finds the change in the slope at the tail of the density
curve, if FALSE, finds it at the head.
alpha
a value in [0,1) specifying the significance of change in the slope
being detected. This is by default 0.1, and typically need not be changed.
sd.threshold
if TRUE, uses 'n.sd' times standard deviation as the threshold.
graphs
if TRUE, generates density distribution plot plus its corresponding threshold.
all.cut
if TRUE, returns all the identified cutoff points, i.e. potential thresholds
for that channel.
tinypeak.removal
A number in [0,1] to exclude/include tiny peaks in density distribution.
adjust.dens
The smoothness of density in [0,Inf] to be used in density(.). The default value is 1 and should not be changed unless necessary