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Global Parametric Time Warping in R Tom Bloemberg The PTW package Institute for Molecules and Materials Dept. Chemometrics / Analytical Chemistry www.ru.nl/imm Global Parametric Time Warping in R The PTW package Chromatographic example

SLIDE 1

The PTW package

Global Parametric Time Warping in R

Tom Bloemberg Institute for Molecules and Materials

Dept. Chemometrics /

Analytical Chemistry www.ru.nl/imm

SLIDE 2

Chromatographic example

The PTW package

Global Parametric Time Warping in R

SLIDE 3

Alignment

Also:

– ‘Synchronization’ – ‘(Time) Warping’

Shift, stretch, compress
Applications in:

– Speech analysis – Chromatography – NMR – …

The PTW package

Global Parametric Time Warping in R

SLIDE 4

Parametric Time Warping1

Before warping:
After warping:
Polynomial model of warping function:
Minimize:

... ) (

2 2 1

+ + + = t a t a a t w

The PTW package

Global Parametric Time Warping in R

∑

=

Q q q qt

a t w ) (

) Sample( ) Reference( t t ↔ )) ( Sample( ) Reference( t w t ↔

( )

∑

−

i i i

t w t

)) ( ( Sample ) ( Reference

SLIDE 5

A single alignment

> library(ptw) > data(chromatograms) > chromatograms <- basel.off(chromatograms) > C.warped <- ptw(chromatograms[1, ], chromatograms[16, ]) > plot(C.warped, plot.orig=TRUE, plot.wf=TRUE)

The PTW package

Global Parametric Time Warping in R

SLIDE 6

> 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 package

Global 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)

SLIDE 7

LC-MS data

The PTW package

Global Parametric Time Warping in R

m/z T T m/z

SLIDE 8

T m/z

LC-MS data

The PTW package

Global Parametric Time Warping in R

m/z T Signal

SLIDE 9

Global Alignment

The PTW package

Global Parametric Time Warping in R

Choose ‘High Quality’ traces using CODA2,3

!""## " !!!

m/z Time

> library(ptw) > data(LCMS) > HQ <- coda(LCMS, combine=c(1,2), windows=c(3,1), nChroms=5) > LCMS.Warped <- ptw(LCMS[1, , ], LCMS[2, , ], HQ=HQ, align.method=“global”)

SLIDE 10

Global Alignment

The PTW package

Global Parametric Time Warping in R

> library(ptw) > data(LCMS) > HQ <- coda(LCMS, combine=c(1,2), windows=c(3,1), nChroms=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), nChroms=5) > LCMS.Warped <- ptw(colSums(LCMS[1, , HQ]), colSums(LCMS[2, , HQ]), align.method = “individual”)

SLIDE 11

Discussion

The PTW package

Global 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)

SLIDE 12

Planning

The PTW package

Global Parametric Time Warping in R

Implement semi-PTW
Implement other distance measures
Connect with dtw-package
Release on 1 September 2009

SLIDE 13

Acknowledgements

Jan Gerretzen Hans Wouters Ron Wehrens Lutgarde Buydens Paul Eilers Jolein Gloerich Hans Wessels Bert van der Heuvel

The PTW package

Global Parametric Time Warping in R