# 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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## Last month downloads

## 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 |

imports | graphics , grDevices , nloptr , stats |

Contributors | Tom Bloemberg Ron Wehrens rwehrenssciencerunl, Hans Wouters, Paul Eilers, Jan Gerretzen |

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