getPeaks: Finding Peaks
In RGLab/flowDensity: Sequential Flow Cytometry Data Gating

Description Usage Arguments Value Author(s) See Also Examples

View source: R/flowDensity_methods.R

Find all peaks in density along with their indices

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

`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.

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

Mehrnoush Malek <mmalekes@bccrc.ca>

deGate notSubFrame flowDensity

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