getPeaks {flowDensity} | R Documentation

## Finding Peaks

### Description

Find all peaks in density along with their indices

### Usage

    getPeaks(obj, channel,tinypeak.removal=1/25, adjust.dens=1,node=NA,verbose=F,twin.factor=1,...)

### Arguments

`obj` | a 'FlowFrame', 'GatingHierarchy', 'CellPopulation' a density object or a numeric vector of density.
`channel` | a channel's name or its corresponding index. If the input is numeric vector, channel is NA.
`tinypeak.removal` | A number in [0,1] to exclude/include tiny peaks in density distribution. Default is 1/25.
`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
`node` | Chareacter for the parent population if passing GatingHierarchy object.
`verbose` | If TRUE, printing warnings.
`twin.factor` | If smaller than 1, peaks that are of greater than hieght as the maximum peak*twin.factor will be removed.
`...` | Arguments passed to smoothSpline function, spar is 0.4.

### Value

a list, including peaks, their corresponding indices and height.

### Author(s)

Mehrnoush Malek <mmalekes@bccrc.ca>

### See Also

`deGate` `notSubFrame` `flowDensity`

### Examples

    data_dir <- system.file("extdata", package = "flowDensity")
    load(list.files(pattern = 'sampleFCS_1', data_dir, full = TRUE))
    #Find the threshold for CD20
    peaks <- getPeaks(f,channel="PerCP-Cy5-5-A",tinypeak.removal=1/30)
    peaks

[Package flowDensity version 1.28.0 Index]