deGate: 1D density gating method
In flowDensity: Sequential Flow Cytometry Data Gating

Description Usage Arguments Value Author(s) 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
3

deGate(flow.frame, channel, n.sd=1.5, use.percentile = FALSE, 
		percentile = 0.95,use.upper=FALSE, upper = NA, talk=TRUE, alpha = 0.1, 
		sd.threshold = FALSE, graphs = FALSE, all.cuts = FALSE, tinypeak.removal=1/25, adjust.dens=1)

`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. Default value is set to 'NA'.
`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'
`talk`	Logical. If TRUE, Prints a message if only one peak is found, or when inflection point is used to set the gates.
`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'.
`graphs`	if TRUE, generates density distribution plot plus its corresponding threshold.
`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.
`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

an integer value (vector) of cutoff(s), i.e. threshold(s), on the specified channel

Jafar Taghiyar <[email protected]>

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)