peakDetect: peakDetect

In mjhelf/Metaboseek: Metaboseek platform

peakDetect

Description

Peak detection using an algorithm modified from Ma et al.[1].

Usage

peakDetect(
  trace,
  SN = 1,
  minwidth = 4,
  localNoise = 7,
  localNoiseFactor = 0.5,
  globalNoiseFactor = 0.5,
  extend = T
)

Arguments

trace	numeric vector of intensity values. it is assumed that the data points were collected in regular intervals (problems may occur e.g. with variable scan rate due to ddMS2 experiments)
SN	factor by which the maximum of a peak has to be larger than its edges (start and end scan) in final filter step
minwidth	minimum width of a peak to not be thrown out in initial filter step
localNoise	window size for local noise level calculation - default 7 means data from each point plus/minus 3 scans is used
localNoiseFactor	factor to adjust local noise level. can be negative to allow very small peaks
globalNoiseFactor	factor to adjust global noise level (based on entire trace). can be negative to allow very small peaks
extend	if true, will try to expand peak boundaries to include downstream tails that may have been cut of before. Aslo depends on local noise settings.

Details

Columns of the returned data.frame:

• max index of position in trace with a peak maximum

• start index of peak start position in trace

• end index of peak end position in trace

Value

a data.frame with detected peaks

References

1. Ma M, van Genderen A, Beukelman P (2005) Developing and Implementing Peak Detection for Real-Time Image Registration. Proc 16th Annu Work Circuits, Syst Signal Process 4:641–652

mjhelf/Metaboseek documentation built on April 23, 2022, 12:09 p.m.