filterPpmError: filterPpmError

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

Description

This function computes an estimate for the ppm error threshold.

Usage

filterPpmError(
  approvedPeaks,
  useGap,
  varExpThresh,
  returnPpmPlots,
  plotDir,
  observedPeak,
  filename
)

Arguments

approvedPeaks	This is a data.frame with information on bins retained after filtering with user input mz error threshold and continuity checks.
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.
observedPeak	A list with names 'start' and 'end' containing scalar values representing the calculated peak boundary points
filename	A string containing the name of the current data file being analyzed.

Details

A distribution is created from the set of all ppm values identified. The most dense peak of this distribution is assumed to represent the standard ppm error of the data.

Value

This function returns a scalar value representing ppm error estimate.

crmclean/AutoTuner documentation built on Jan. 29, 2021, 4:48 p.m.