retcor-methods {xcms} | R Documentation |
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 xcmsSet object |
plottype |
if deviation plot retention time deviation points and
regression fit, and if mdevden also plot peak overall
peak density and retention time correction peak density
|
col |
vector of colors for plotting each sample |
ty |
vector of line and point types for plotting each sample |
profStep |
step size (in m/z) to use for profile generation from the raw data files |
r |
Responsiveness of warping. 0 will give a linear warp based on start and end points. 100 will use all bijective anchors |
g |
Gap penalty given in comma separated string: initiate,extend (*)Defaults: (gap_init,gap_extend) [by score type]: 'cor' = '0.3,2.4' 'cov' = '0,11.7' 'prd' = '0,7.8' 'euc' = '0.9,1.8' |
cor |
Score function: (*)cor (Pearson's R) or cor_opt (better runtime), cov (covariance), prd (product), euc (Euclidean distance) |
l |
Local rather than *global alignment |
i_ |
Penalty for initiating alignment (for local alignment only) (*)Default: 0 |
An xcmsSet
object