Align retention times across samples with Obiwarp

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

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)

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

See also

xcmsSet-class,