deGate {flowDensity} | R Documentation

## 1D density gating method

### Description

Find the best threshold for a single channel in flow cytometry data based on its density distribution.

### Usage

    deGate(obj,channel, n.sd = 1.5, use.percentile = FALSE,  percentile =NA,use.upper=FALSE, upper = NA,verbose=TRUE,twin.factor=.98,
                       bimodal=F,after.peak=NA,alpha = 0.1, sd.threshold = FALSE, all.cuts = FALSE,
                       tinypeak.removal=1/25,node=NA, adjust.dens = 1,count.lim=20,magnitude=.3,slope.w=4, ...)

### Arguments

`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 is NA. If set to a value(n) and use.percentile=F, it returns the n-th percentile, for 1-peak populations.
`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
`slope.w` | window.width for tracking slope. Default is 4, calculating a slope based on 4 points before and after the current point.
`...` | Extra arguments to be passed to smoothSpline function.

### Details

deGate works for GatingHierarchy, flowFrame, CellPopulation object or a numeric vector of data. In case the input is a numeric vector, channel doesn't need to provided, but the rest of arguments can be used to tune the outcome.

### Value

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

### Author(s)

Mehrnoush Malek <mmalekes@bccrc.ca>

### See Also

`getflowFrame` `notSubFrame` `flowDensity`

### Examples

    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)

[Package flowDensity version 1.20.0 Index]