Description Usage Arguments Value Author(s) See Also Examples
View source: R/flowDensity_methods.R
Find the best threshold for a single channel in flow cytometry data based on its density distribution.
1 2 |
obj |
obj: a 'FlowFrame' object, 'CellPopulation' or 'GatingHierarchy' |
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. |
use.upper |
Logical. If TRUE, forces to return the inflection point based on the first (last) peak if upper=F (upper=T). Default value is set to 'FALSE' |
upper |
if TRUE, finds the change in the slope at the tail of the density curve, if FALSE, finds it at the head. Default value is set to 'NA'. |
verbose |
Logical. If TRUE, Prints a message if only one peak is found, or when inflection point is used to set the gates. |
twin.factor |
a value in [0,1] that is used to exclude twinpeaks |
bimodal |
Logical. If TRUE, it returns a cutoff that splits population closer to 50-50, when there are more than two peaks. |
after.peak |
Logical. If TRUE, it returns a cutoff that is after the maximum peaks, when there are more than two peaks. |
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. Default value is set to 'FALSE'. |
all.cuts |
if TRUE, returns all the identified cutoff points, i.e. potential thresholds for that channel. Default value is set to 'FALSE'. |
tinypeak.removal |
A number in [0,1] to exclude/include tiny peaks in density distribution. |
node |
A character defining the parent population when extracting data from GatingHierarchy. |
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 |
count.lim |
minimum limit for events count in order to calculate the threshold. Default is 20, returning NA as threshold. |
magnitude |
A value between 0 and 1, for tracking a slope and reporting changes that are smaller than magnitude*peak_height |
... |
Extra arguments to be passed to smoothSpline function. |
an integer value (vector) of cutoff(s), i.e. threshold(s), on the specified channel
Mehrnoush Malek <[email protected]>
getflowFrame
notSubFrame
flowDensity
1 2 3 4 5 6 7 | data_dir <- system.file("extdata", package = "flowDensity")
load(list.files(pattern = 'sampleFCS_1', data_dir, full = TRUE))
#Find the threshold for CD20
cd19.gate <- deGate(f,channel="PerCP-Cy5-5-A")
# Gate out the CD20- populations using the notSubFrame
plotDens(f,c("APC-H7-A","PerCP-Cy5-5-A"))
abline(h=cd19.gate,lty=3,col=2)
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