retcor.obiwarp {xcms} | R Documentation

## Align retention times across samples with Obiwarp

### Description

Calculate retention time deviations for each sample. It is based on the code at http://obi-warp.sourceforge.net/. However, this function is able to align multiple samples, by a center-star strategy.

For the original publication see

Chromatographic Alignment of ESI-LC-MS Proteomics Data Sets by Ordered Bijective Interpolated Warping John T. Prince and, Edward M. Marcotte Analytical Chemistry 2006 78 (17), 6140-6152

### Arguments

`object` | the `xcmsSet` object
`plottype` | if `deviation` plot retention time deviation
`profStep` | step size (in m/z) to use for profile generation from the raw data files
`center` | the index of the sample all others will be aligned to. If center==NULL, the sample with the most peaks is chosen as default.
`col` | vector of colors for plotting each sample
`ty` | vector of line and point types for plotting each sample
`response` | Responsiveness of warping. 0 will give a linear warp based on start and end points. 100 will use all bijective anchors
`distFunc` | DistFunc function: cor (Pearson's R) or cor_opt (default, calculate only 10% diagonal band of distance matrix, better runtime), cov (covariance), prd (product), euc (Euclidean distance)
`gapInit` | Penalty for Gap opening, see below
`gapExtend` | Penalty for Gap enlargement, see below
`factorDiag` | Local weighting applied to diagonal moves in alignment.
`factorGap` | Local weighting applied to gap moves in alignment.
`localAlignment` | Local rather than global alignment
`initPenalty` | Penalty for initiating alignment (for local alignment only) Default: 0

Default gap penalties: (gapInit, gapExtend) [by distFunc type]: 'cor' = '0.3,2.4' 'cov' = '0,11.7' 'prd' = '0,7.8' 'euc' = '0.9,1.8'

### Value

An `xcmsSet` object

### Methods

object = "xcmsSet"

  retcor(object, method="obiwarp", plottype = c("none", "deviation"), profStep=1, center=NULL, col = NULL, ty = NULL, response=1, distFunc="cor_opt", gapInit=NULL, gapExtend=NULL, factorDiag=2, factorGap=1, localAlignment=0, initPenalty=0)

### See Also

`xcmsSet-class`,

[Package xcms version 3.9.1 Index]