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,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 <[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 May 1, 2022, 12:50 p.m.