getPeaks: Finding Peaks

Description Usage Arguments Value Author(s) See Also Examples

View source: R/flowDensity_methods.R

Description

Find all peaks in density along with their indices

Usage

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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 <[email protected]>

See Also

deGate notSubFrame flowDensity

Examples

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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

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