madFilter {flowSpecs} | R Documentation

## Median absolute deviation-based automatic filters for flowCore objects

### Description

This function is meant to create conservative, MAD-based filters for n-peaked cytometry variables. The function is so far not flowCore-compliant, and thus not available as a direct user function, but only used internally. This will change soon.

### 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.

[Package flowSpecs version 1.1.2 Index]