EICparams: EICparams

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

Description

This function is designed to calculate the recommended parameters from EIC peaks. It is the main holder function for a lot of different ones involved in calculating EIC parameters.

Usage

EICparams(
  Autotuner,
  massThresh,
  useGap = TRUE,
  varExpThresh = 0.8,
  returnPpmPlots = TRUE,
  plotDir = ".",
  verbose = TRUE
)

Arguments

Autotuner	An Autotuner objected containing sample specific raw data.
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	A boolean value that tells R to return plots for ppm distributions.
plotDir	Path where to store plots.
verbose	Boolean value used to indicate whether checkEICPeaks function returns messages to the console.

Details

The function CheckEICPeaks handles all the peak specific computations.

Value

A data.frame of all peak specific estimates.

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