madFilter: Median absolute deviation-based automatic filters for...

In jtheorell/theFlowSpec: Tools for spectral unmixing of overdetermined flow-cytometry files. And other nice things.

Description

This function is meant to create conservative, MAD-based filters for n-peaked cytometry variables.

Usage

madFilter(flowObj, gateVar = 1, nMads = 2, filterName = "default",
  nGates = 1, madSide = "both", adjust = 2,
  nonMadFilter = "deflection", returnSepFilter = FALSE)

Arguments

flowObj	The fcs object to be filtered. Both flowFrames and flowSets are accepted.
gateVar	The variable that should be used to set the gate. Can either be an integer or a string.
nMads	The number of median absolute deviations that should be included. These are calculated separately from each half of the peak, so if applied on both sides, there can still be an assymetry present.
filterName	The common name to the filter(s) created by the function. Default is the name of the gate variable.
nGates	The number of gates that should be produced
madSide	Which side of the peak(s) should the MAD filter be applied to? "low", "high", "both" and "none" supported.
adjust	The value deciding the accuracy of the density calculation. The higher the value, the lower the sensitivity for small aberrations in the density.
nonMadFilter	What filter should be applied on the possible non-mad side? The three alternatives are: "deflection" Here, the gate is extended to the deflection point marking the start of the next peak. "none" and "default". "none" Here, all events are included It is worth noting that madSide overrides this argument.
returnSepFilter	Should the gate be returned as a separate object? Currently, this defaults to FALSE.

Value

flowObject of the same class as flowObj with the gates added as boolean variables to the exprs portions of the flowFrames.

jtheorell/theFlowSpec documentation built on Aug. 22, 2019, 3:33 a.m.