Description Arguments Value Methods See Also
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
object |
the |
plottype |
if |
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'
An xcmsSet
object
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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.