Table A.4.
Arguments of the built-in function deGate - adapted from the vignette of flowDensity
| 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. 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. |