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Last data update: 2014.03.03

R: Identify ridges based on the local maximum matrix

getRidge

R Documentation

Identify ridges based on the local maximum matrix

Description

Identify ridges by connecting the local maximum of 2-D CWT coefficients from the coarse scale to detail scale. The local maximum matrix is returned from getLocalMaximumCWT

Usage

getRidge(localMax, iInit = ncol(localMax), step = -1, iFinal = 1, minWinSize= 5, gapTh = 3, skip = NULL)

Arguments

`localMax`	The local maximum matrix is returned from `getLocalMaximumCWT` with 1 represents maximum, others are 0.
`iInit`	The start column to search ridge. By default, it starts from the coarsest scale level.
`step`	Search step. -1 by default, which means searching from coarse scale to detail scale column by column.
`iFinal`	The final column index of search ridge.
`minWinSize`	The minimum slide window size used.
`gapTh`	The gap allowed during searching for ridge. 3 by default.
`skip`	The column to be skipped during search.

Value

Return a list of ridge. As some ridges may end at the scale larger than 1, in order to keep the uniqueness of the ridge names, we combined the smallest scale of the ridge and m/z index of the peak at that scale together to name the ridges. For example the ridge name "1_653" means the peak ridge ends at the CWT scale 1 with m/z index 653 at scale 1.

Author(s)

Pan Du, Simon Lin

References

Du, P., Kibbe, W.A. and Lin, S.M. (2006) Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching, Bioinformatics, 22, 2059-2065.

Examples

	data(exampleMS)
	scales <- seq(1, 64, 3)
	wCoefs <- cwt(exampleMS[5000:11000], scales=scales, wavelet='mexh')
	
	localMax <- getLocalMaximumCWT(wCoefs)
	ridgeList <- getRidge(localMax)
	plotRidgeList(ridgeList)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(MassSpecWavelet)
Loading required package: waveslim

waveslim: Wavelet Method for 1/2/3D Signals (version = 1.7.5)

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MassSpecWavelet/getRidge.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getRidge
> ### Title: Identify ridges based on the local maximum matrix
> ### Aliases: getRidge
> ### Keywords: methods
> 
> ### ** Examples
> 
> 	data(exampleMS)
> 	scales <- seq(1, 64, 3)
> 	wCoefs <- cwt(exampleMS[5000:11000], scales=scales, wavelet='mexh')
> 	
> 	localMax <- getLocalMaximumCWT(wCoefs)
> 	ridgeList <- getRidge(localMax)
> 	plotRidgeList(ridgeList)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>