peakIdenti: Peak identification for higher-level functions.

In jtheorell/flowSpecs: Tools for processing of high-dimensional cytometry data

Peak identification for higher-level functions.

Description

This function is primarily thought to be used internally to define peaks in data. One function is borrowed from package vulcan, namely the vulcan::densityauc, which is neat, but the package is large and significantly increases the installation time, and the importing is thus discarded.

Usage

peakIdenti(
  markerData,
  volThresh = 0.05,
  distThresh = 0.1,
  adjust = 2,
  nPeaks = 2,
  returnStats = FALSE
)

Arguments

markerData	The data that the peaks should be identified for
volThresh	The cutoff ratio of the volume for each secondary peak, under which it is not considered to be a peak
distThresh	The cutoff under which two peaks are considered one, as they are too close to each other. This value between 0 and 1 corresponds to a fraction from the 10th to the 90th percentile of the data range that the peaks must be separated by to count. Defaults to 0.1 or 10 percent of the distance.
adjust	The value deciding the accuracy of the density calculation. The higher the value, the lower the sensitivity for small aberrations in the density.
nPeaks	The number of peaks that should be exported. If n+1 fulfilling the volRatio criterion are found, the peaks most separated in space are chosen.
returnStats	Should the deflection points defining the peaks, the peak hight and the lowest deflection point between the two most extreme peaks be included in the export?

Value

The information about the peaks in question. Depending on if returnStats is TRUE or not and the number of peaks, it will change in complexity.

See Also

densityauc

jtheorell/flowSpecs documentation built on April 24, 2023, 2:59 a.m.