getPeaks: Finding Peaks

In mehrnoushmalek/flowDensity: Sequential Flow Cytometry Data Gating

Finding Peaks

Description

Find all peaks in density along with their indices

Usage

getPeaks(obj, channel,tinypeak.removal=1/25, adjust.dens=1,verbose=F,twin.factor=1,spar = 0.4,...)

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
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.
spar	argument to pass to smoothSpline function, default value of spar is 0.4.
...	Other arguments that can be passed to smoothSpline function.

Value

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

Author(s)

Mehrnoush Malek <[e-mail]>

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

mehrnoushmalek/flowDensity documentation built on Oct. 31, 2023, 1:27 a.m.