calculateModality: Calculate Modality (of a Chromatographic Peak)

In KelseyChetnik/MetaClean: Detection of Low-Quality Peaks in Untargeted Metabolomics Data

Description

Calculates the Modality of the integrated region of a chromatographic peak. The Modaily is found by taking the ratio of the magnitude of the largest drop in intensity (exluding the apex) and the maximum intensity of the peak.

Usage

calculateModality(peakData, pts, flatness.factor = 0.05)

Arguments

peakData	A vector containing characteristic information about a chromatographic peak - including the retention time range
pts	A 2D matrix containing the retention time and intensity values of a chromatographic peak
flatness.factor	A numeric value between 0 and 1 that allows the user to adjust the sensitivity of the function to noise. This function calculates the difference between each adjacent pair of points; any value found to be less than flatness.factor * maximum intensity is set to 0.

Details

This function repurposed from TargetedMSQC. Toghi Eshghi, S., Auger, P., & Mathews, W. R. (2018). Quality assessment and interference detection in targeted mass spectrometry data using machine learning. Clinical Proteomics, 15. https://doi.org/10.1186/s12014-018-9209-x

Value

The modality of the peak (double)

Examples

# Calculate Modality for a peak
data(ex_pts)
data(ex_peakData)
modality <- calculateModality(peakData = ex_peakData, pts = ex_pts)

KelseyChetnik/MetaClean documentation built on May 17, 2021, 5:33 a.m.