# Automated Optimization of XCMS Data Processing parameters

## Documentation for package ‘IPO’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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