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
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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

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