# ptw v1.9-15

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## Parametric Time Warping

Parametric Time Warping aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation). Both warping of peak profiles and of peak lists are supported. A vignette for the latter is contained in the inst/doc directory of the source package - the vignette source can be found on the package github site.

## Functions in ptw

 Name Description bestref Identification of optimal reference asysm Trend estimation with asymmetric least squares coda Chromatogram selection using the CODA algorithm gaschrom 16 calibration GC traces lcms Parts of 3 proteomic LC-MS samples RMS Quality criteria for comparing patterns with shifts baseline.corr Baseline Correction using asymmetric least squares calc.multicoef Calculation of warping coefficients when applying more than one warping function successively difsm Smoothing with a finite difference penalty calc.zerocoef Correction for warping coefficients when using zeropadding plot.ptw Plot a ptw object ptw-package ptw ptw Parametric Time Warping padzeros Pad matrix with zeros mzchannel2pktab Conversion between peak lists from hyphenated MS (LCMS, GCMS, ...) data and input for stptw. whit1 Weighted Whittaker smoothing with a first order finite difference penalty whit2 Weighted Whittaker smoothing with a second order finite difference penalty wcc Weighted auto- and cross-correlation measures warp.time Transform time according to a given warping function predict.ptw Prediction of warped signals select.traces Select traces from a data set according to several criteria ptwgrid Calculate RMS or WCC values on a grid No Results!

## Details

 Type Package URL https://github.com/rwehrens/ptw License GPL (>= 2) NeedsCompilation yes Packaged 2019-11-26 11:06:01 UTC; ron Repository CRAN Date/Publication 2019-11-26 14:20:02 UTC
 imports graphics , grDevices , nloptr , stats Contributors Tom Bloemberg Ron Wehrens rwehrenssciencerunl, Hans Wouters, Paul Eilers, Jan Gerretzen