Automated Optimization of XCMS Data Processing parameters

Documentation for package ‘IPO’ version 1.14.0

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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