ptw: 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.

Author
Jan Gerretzen <j.gerretzen@science.ru.nl>, Paul Eilers <p.eilers@erasmusmc.nl>, Hans Wouters, Tom Bloemberg <t.bloemberg@science.ru.nl>, Ron Wehrens <ron.wehrens@gmail.com>
Date of publication
2015-08-21 11:48:26
Maintainer
Ron Wehrens <ron.wehrens@gmail.com>
License
GPL (>= 2)
Version
1.9-11

View on CRAN

Man pages

asysm
Trend estimation with asymmetric least squares
baseline.corr
Baseline Correction using asymmetric least squares
bestref
Identification of optimal reference
calc.multicoef
Calculation of warping coefficients when applying more than...
calc.zerocoef
Correction for warping coefficients when using zeropadding
coda
Chromatogram selection using the CODA algorithm
difsm
Smoothing with a finite difference penalty
gaschrom
16 calibration GC traces
lcms
Parts of 3 proteomic LC-MS samples
mzchannel2pktab
Conversion between peak lists from hyphenated MS (LCMS, GCMS,...
padzeros
Pad matrix with zeros
plot.ptw
Plot a ptw object
predict.ptw
Prediction of warped signals
ptw
Parametric Time Warping
ptwgrid
Calculate RMS or WCC values on a grid
RMS
Quality criteria for comparing patterns with shifts
select.traces
Select traces from a data set according to several criteria
warp.time
Transform time according to a given warping function
wcc
Weighted auto- and cross-correlation measures
whit1
Weighted Whittaker smoothing with a first order finite...
whit2
Weighted Whittaker smoothing with a second order finite...

Files in this package

ptw
ptw/TODO
ptw/inst
ptw/inst/CITATION
ptw/inst/NEWS
ptw/inst/doc
ptw/inst/doc/stickPTW.pdf
ptw/inst/doc/stickPTW.Rnw
ptw/src
ptw/src/approx.c
ptw/src/smth.c
ptw/src/wcc.c
ptw/src/wccStick.c
ptw/NAMESPACE
ptw/demo
ptw/demo/demo1.R
ptw/demo/demo2.R
ptw/demo/demo3.R
ptw/demo/00Index
ptw/data
ptw/data/gaschrom.RData
ptw/data/lcms.RData
ptw/data/datalist
ptw/R
ptw/R/select.traces.R
ptw/R/whit2.R
ptw/R/calc.multicoef.R
ptw/R/baseline.corr.R
ptw/R/plot.ptw.R
ptw/R/calc.zerocoef.R
ptw/R/bestref.R
ptw/R/ptw.R
ptw/R/difsm.R
ptw/R/wccStick.R
ptw/R/padzeros.R
ptw/R/predict.ptw.R
ptw/R/summary.ptw.R
ptw/R/RMS.R
ptw/R/WCC.R
ptw/R/whit1.R
ptw/R/asysm.R
ptw/R/pmwarp.R
ptw/R/coda.R
ptw/R/warp.sample.R
ptw/R/ptwgrid.R
ptw/vignettes
ptw/vignettes/stickPTW-010.pdf
ptw/vignettes/stickPTW-004.pdf
ptw/vignettes/stickPTW-002.pdf
ptw/vignettes/stickPTW-013.pdf
ptw/vignettes/stickPTW-011.pdf
ptw/vignettes/stickPTW-025.pdf
ptw/vignettes/stickPTW-003.pdf
ptw/vignettes/ptwbib.bib
ptw/vignettes/stickPTW-019.pdf
ptw/vignettes/stickPTW-009.pdf
ptw/vignettes/stickPTW-012.pdf
ptw/vignettes/stickPTW.Rnw
ptw/MD5
ptw/build
ptw/build/vignette.rds
ptw/DESCRIPTION
ptw/man
ptw/man/calc.multicoef.Rd
ptw/man/ptw.Rd
ptw/man/calc.zerocoef.Rd
ptw/man/wcc.Rd
ptw/man/plot.ptw.Rd
ptw/man/predict.ptw.Rd
ptw/man/lcms.Rd
ptw/man/baseline.corr.Rd
ptw/man/mzchannel2pktab.Rd
ptw/man/difsm.Rd
ptw/man/select.traces.Rd
ptw/man/whit1.Rd
ptw/man/padzeros.Rd
ptw/man/warp.time.Rd
ptw/man/gaschrom.Rd
ptw/man/bestref.Rd
ptw/man/coda.Rd
ptw/man/asysm.Rd
ptw/man/RMS.Rd
ptw/man/ptwgrid.Rd
ptw/man/whit2.Rd