'use.percentile' if TRUE, returns the 'percentile'th threshold.
'percentile' a value in [0,1] that is used as the percentile if 'use.percentile' is TRUE.
'upper' if 'TRUE', it finds the change in the slope after the peak with index 'peak.ind'.
'use.upper' if 'TRUE', forces to return the inflection point based on the first (last) peak if upper=F (upper=T)
'twin.factor' a value in [0,1] that is used to exclude twinpeaks.
'bimodal' If TRUE, it returns a cutoff that splits population closer to 50-50, when there are more than two peaks.
'after.peak' If TRUE, it returns a cutoff that is after the maximum peaks, when there are more than two peaks.
'sd.threshold' if TRUE, it uses 'n.sd' times standard deviation for gating.
'n.sd' an integer that is multiplied to the standard deviation to determine the place
of threshold if 'sd.threshold' is 'TRUE'.
'tinypeak.removal' a vector of length 2, for sensitivity of peak finding for each channel. See deGate() for more information.
'filter' If provided it uses the given filter to gate the population.
'use.control' if TRUE, it finds the threshold using a matched control population and uses it for gating.
'control' a 'flowFrame' or 'CellPopulation' object used for calculating the gating threshold when
'use.control' is set to TRUE. If a control population is used, the other arguments ('upper', 'percentile',
etc.) are applied to the control data when finding the threshold (i.e. not to 'obj').
'alpha' a value in [0,1) specifying the significance of change in the slope
which would be detected. This is by default 0.1, and typically need not be changed.
'ellip.gate' if TRUE, it fits an ellipse on the data as a gate, otherwise the
rectangle gating results are returned
'scale' a value in [0,1) that scales the size of ellipse to fit if 'ellip.gate' is TRUE