flowDensity-methods: Methods for Function 'flowDensity' in Package 'flowDensity'

Description Usage Arguments Value

Description

Methods for function flowDensity in package flowDensity

Usage

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## S4 method for signature 'CellPopulation,ANY,logical,missing'
flowDensity(obj, channels, position,node, ...)
## S4 method for signature 'flowFrame,ANY,logical,missing'
flowDensity(obj, channels, position,node, ...)
## S4 method for signature 'GatingHierarchy,ANY,logical,ANY'
flowDensity(obj, channels, position,node, ...)

Arguments

obj

GatingHierarchy or CellPopulationobject

channels

a vector of two channel names or their corresponding indices.

position

a vector of two logical values specifying the position of the cell subset of interest on the 2D plot.

node

A character defining the parent population when extracting data from GatingHierarchy.

...

This can be used to pass one of the following arguments:

  • '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

Value

a CellPopulation object.


mehrnoushmalek/flowDensity documentation built on Oct. 26, 2019, 2:26 p.m.