CalculatePeakJaggedness: Compute jaggedness scores for transition peaks in a peak...

In shadieshghi/TargetedMSQC: TargetedMSQC for Automated Quality Assessment of Targeted Mass Spectrometry Data

Description

The function takes a peak group of class peakObj as input and calculates the jaggedness score for the transition peaks in the peak group using the CalculateJaggedness function. The jaggedness score is defined as the fraction of timepoints where the signal changes direction, excluding the change of direction at the peak apex. For high quality peaks, the jaggedness score is expected to be close to 0.

Usage

CalculatePeakJaggedness(peak, flatness.factor = 0.05, ...)

Arguments

peak

A peak group of class peakObj

flatness.factor

A numeric parameter between 0 and 1 that determines the sensitivity of the jaggedness score to low levels of noise. To avoid high jaggedness scores due to small levels of noise, near-flat ranges in the peak are artificially flattened before calculating the jaggedness score. A range is defined as near-flat and thus flattened when the difference between intensities of adjacent time points is smaller than flatness.factor times the peak maximum intensity.

Value

A list with the following objects: r.jaggedness: A numeric vector of jaggedness scores for each transition in the peak group. peak.jaggedness: Mean of the r.jaggedness vector. This score represents the overall jaggedness of all the transitions in the peak group.

Examples

peak <- data.CSF$data$PeakGroup[[196]]
peak.group.jaggedness <- CalculatePeakJaggedness(peak)

shadieshghi/TargetedMSQC documentation built on May 13, 2019, 12:20 p.m.