Global Parametric Time Warping in R The PTW package · The PTW package Global Parametric Time...
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The PTW package Global Parametric Time Warping in R Tom Bloemberg Institute for Molecules and Materials Dept. Chemometrics / Analytical Chemistry www.ru.nl/imm
Transcript of Global Parametric Time Warping in R The PTW package · The PTW package Global Parametric Time...
The PTW packageGlobal Parametric Time Warping in RTom Bloemberg
Institute for Molecules and Materials
Dept. Chemometrics / Analytical Chemistry
www.ru.nl/imm
Chromatographic example
The PTW packageGlobal Parametric Time Warping in R
Alignment
• Also: – ‘Synchronization’
– ‘(Time) Warping’
• Shift, stretch, compress• Applications in:
– Speech analysis
– Chromatography– NMR
– …
The PTW packageGlobal Parametric Time Warping in R
Parametric Time Warping1
• Before warping:
• After warping:
• Polynomial model of warping function:
• Minimize:
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The PTW packageGlobal Parametric Time Warping in R
1 Eilers, P.H.C. Analytical Chemistry 76 (2) 404-411 2004
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A single alignment
> library(ptw)
> data(chromatograms)
> chromatograms <- basel.off(chromatograms)
> C.warped <- ptw(chromatograms[1, ], chromatograms[1 6, ])
> plot(C.warped, plot.orig=TRUE, plot.wf=TRUE)
The PTW packageGlobal Parametric Time Warping in R
> library(ptw)
> data(chromatograms)
> chromatograms <- basel.off(chromatograms)
> C.warped <- ptw(chromatograms[1:8, ], chromatograms [9:16, ])
> plot(C.warped, plot.orig=TRUE, plot.wf=TRUE)
Multiple alignments
The PTW packageGlobal Parametric Time Warping in R
> library(ptw)
> data(chromatograms)
> chromatograms <- basel.off(chromatograms)
> C.warped <- ptw(chromatograms[1, ], chromatograms[2 :16, ])
> plot(C.warped, plot.orig=TRUE, plot.wf=TRUE)
LC-MS data
The PTW packageGlobal Parametric Time Warping in R
m/z
T
T
m/z
Tm/z
LC-MS data
The PTW packageGlobal Parametric Time Warping in R
m/z
T
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nal
Global Alignment
The PTW packageGlobal Parametric Time Warping in R
• Choose ‘High Quality’ traces using CODA2,3
2Windig, W. Analytical Chemistry 68 (20) 3602-3606 1996
3Christin, C. Analytical Chemistry 80 (18) 7012-7021 2008
m/z
Time> library(ptw)
> data(LCMS)
> HQ <- coda(LCMS, combine=c(1,2), windows=c(3,1), n Chroms=5)
> LCMS.Warped <- ptw(LCMS[1, , ], LCMS[2, , ], HQ=HQ, align.method=“global”)
Global Alignment
The PTW packageGlobal Parametric Time Warping in R
> library(ptw)
> data(LCMS)
> HQ <- coda(LCMS, combine=c(1,2), windows=c(3,1), n Chroms=5)
> LCMS.Warped <- ptw(LCMS[1,,], LCMS[2,,], HQ=HQ, align.method = “global”)
> library(ptw)
> data(LCMS)
> HQ <- coda(LCMS, combine=c(1,2), windows=c(3,1), n Chroms=5)
> LCMS.Warped <- ptw(colSums(LCMS[1, , HQ]), colSums(LCMS[2, , HQ]), align.method = “individual”)
Discussion
The PTW packageGlobal Parametric Time Warping in R
• Second alignment package for R (next to dtw)
• Individual, multiple and global warpings• Trace selection (CODA)• Baseline removal (asymmetric LS)• Smoothing (Whittaker)
Planning
The PTW packageGlobal Parametric Time Warping in R
• Implement semi-PTW
• Implement other distance measures• Connect with dtw-package• Release on 1 September 2009
Acknowledgements
Jan Gerretzen
Hans WoutersRon WehrensLutgarde Buydens
Paul Eilers
Jolein GloerichHans WesselsBert van der Heuvel
The PTW packageGlobal Parametric Time Warping in R
