ptw: Parametric Time Warping
Version 1.9-12

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.

Browse man pages Browse package API and functions Browse package files

AuthorJan 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 publication2017-03-06 11:28:52
MaintainerRon Wehrens <ron.wehrens@gmail.com>
LicenseGPL (>= 2)
Version1.9-12
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ptw")

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...

Functions

RMS Man page Source code
STWCC Source code
WCC Man page Source code
asysm Man page Source code
baseline.corr Man page Source code
bestref Man page Source code
calc.multicoef Man page Source code
calc.zerocoef Man page Source code
coda Man page Source code
coef.ptw Man page Source code
difsm Man page Source code
gaschrom Man page
gaschrom.st Man page
lcms Man page
lcms.pks Man page
mz Man page
mzchannel2pktab Man page Source code
padzeros Man page Source code
pktab2mzchannel Man page Source code
plot.ptw Man page Source code
plot.stptw Source code
pmwarp Source code
predict.ptw Man page Source code
print.ptw Man page Source code
print.stptw Man page Source code
ptw Man page Source code
ptwgrid Man page Source code
select.traces Man page Source code
stptw Man page Source code
stwarp Source code
summary.ptw Man page Source code
summary.stptw Man page Source code
time Man page
wac Man page Source code
wac.st Man page Source code
warp.sample Source code
warp.time Man page Source code
wcc Man page Source code
wcc.st Man page Source code
whit1 Man page Source code
whit2 Man page Source code

Files

TODO
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/stickPTW.pdf
inst/doc/stickPTW.Rnw
src
src/register.c
src/approx.c
src/smth.c
src/wcc.c
src/wccStick.c
NAMESPACE
demo
demo/demo1.R
demo/demo2.R
demo/demo3.R
demo/00Index
data
data/gaschrom.RData
data/lcms.RData
data/datalist
R
R/select.traces.R
R/whit2.R
R/calc.multicoef.R
R/baseline.corr.R
R/plot.ptw.R
R/calc.zerocoef.R
R/bestref.R
R/ptw.R
R/difsm.R
R/wccStick.R
R/padzeros.R
R/predict.ptw.R
R/summary.ptw.R
R/RMS.R
R/WCC.R
R/whit1.R
R/asysm.R
R/pmwarp.R
R/coda.R
R/warp.sample.R
R/ptwgrid.R
vignettes
vignettes/stickPTW-010.pdf
vignettes/stickPTW-004.pdf
vignettes/stickPTW-002.pdf
vignettes/stickPTW-013.pdf
vignettes/stickPTW-011.pdf
vignettes/stickPTW-025.pdf
vignettes/stickPTW-003.pdf
vignettes/ptwbib.bib
vignettes/stickPTW-019.pdf
vignettes/stickPTW-009.pdf
vignettes/stickPTW-012.pdf
vignettes/stickPTW.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/calc.multicoef.Rd
man/ptw.Rd
man/calc.zerocoef.Rd
man/wcc.Rd
man/plot.ptw.Rd
man/predict.ptw.Rd
man/lcms.Rd
man/baseline.corr.Rd
man/mzchannel2pktab.Rd
man/difsm.Rd
man/select.traces.Rd
man/whit1.Rd
man/padzeros.Rd
man/warp.time.Rd
man/gaschrom.Rd
man/bestref.Rd
man/coda.Rd
man/asysm.Rd
man/RMS.Rd
man/ptwgrid.Rd
man/whit2.Rd
ptw documentation built on May 29, 2017, 2:27 p.m.