checkEICPeaks: checkEICPeaks

In crmclean/Autotuner: Automated parameter selection for untargeted metabolomics data processing

Description

This function is the outer most function used to check for individual EIC peak specific parameters.

Usage

checkEICPeaks(
  mzDb,
  header,
  observedPeak,
  massThresh = 0.005,
  useGap,
  varExpThresh,
  returnPpmPlots,
  plotDir,
  filename
)

Arguments

mzDb	A list of data.frames containing the m/z and intensity values from each scan's mass spectra.
header	A data.fame containing metadata on the sample like spectra type, retention time, and scan count.
observedPeak	A list with names 'start' and 'end' containing scalar values representing the calculated peak boundary points
massThresh	A generous exact mass error threshold used to estimate PPM for features.
useGap	Parameter carried into checkEICPeaks that tells Autotuner whether to use the gap statustic to determine the proper number of clusters to use during ppm parameter estimation.
varExpThresh	Numeric value representing the variance explained threshold to use if useGap is false.
returnPpmPlots	Boolean value that tells R to return plots for ppm distributions.
plotDir	Path where to store plots.
filename	A string containing the name of the current data file being analyzed.

Value

This function returns a peak specific set of processign parameters.

crmclean/Autotuner documentation built on Jan. 23, 2021, 1:43 a.m.