retcor.obiwarp-methods: Align retention times across samples with Obiwarp

In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

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,

xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.