Automated Optimization of XCMS Data Processing parameters

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Documentation for package ‘IPO’ version 1.28.0

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IPO-package Automated Optimization of Untargeted Metabolomics LC-MS Data Processing
attachList Attaching one list at the end of another
calcPPS Calculation of a peak picking score (PPS) by using natural, stable 13C isotopes
calculateXcmsSet Calculation of an xcmsSet-Object
combineParams Combining two lists of parameters together.
createModel Creating a response surface model.
decode En-/decodes values to/from ranges of -1 to 1.
decodeAll En-/decodes values to/from ranges of -1 to 1.
encode En-/decodes values to/from ranges of -1 to 1.
findIsotopes.CAMERA Identification of Isotopes using the package CAMERA.
findIsotopes.IPO Identification of 13C isotopes
getBbdParameter Creates a Box-Behnken Design of experiment
getCcdParameter Creates a Central-Composite Design of experiment
getDefaultRetCorCenterSample Gets the index of the sample with most peaks in it.
getDefaultRetGroupStartingParams Gives a List of parameters for xcms-methods retcor.obiwarp or retcor.loess and group.density which are optimized by default
getDefaultXcmsSetStartingParams Creates a List of parameters for xcms-methods xcmsSet.findPeak which are optimized by default
getNormalizedResponse It combines Retention time Correction Scores (RCS) and Grouping Scores (GS)
getRGTVValues Calculation of values used for a Retention time correction and Grouping Target Value (RGTV)
IPO Automated Optimization of Untargeted Metabolomics LC-MS Data Processing
optimizeRetGroup Optimization for parameters for retention time correction and grouping
optimizeXcmsSet Optimisation of peak picking parameters by using natural, stable 13C isotopes
toMatrix Converts an array into a matrix
typeCastParams Splits parameters into those which should be optimized and those which are fixed.
writeParamsTable Writes XCMS settings to a file.
writeRScript Prints an R-script to the screen which can be used for xcms processing